Why is Mavericks running so slowly after a fresh install on my Macbook Pro?

Question

I have a 13-inch, Early 2011 Macbook Pro.
Towards the end of 2013 Mountain Lion had been running very sluggishly, and I was getting the spinning beachball of death all the time, so I decided to do a fresh install of Mavericks. I wiped my whole HD using disk utility and installed Mavericks from a flash drive.
I then installed Microsoft Office 2011 from the original DVD and set up Mac Mail to work with my Gmail account etc. All very standard. I also installed X-Code and various other things related to my work, but nothing crazy. My HD is only half-full (I have 141 GB of free space).
Despite this, everything is running really sluggishly (especially when MS Office programs are open) and I have to watch the beachball of death spin for about 10 seconds every minute.
Any help is greatly appreciated!
Here is the Etrecheck output:
Hardware Information:
          MacBook Pro (13-inch, Early 2011)
          MacBook Pro - model: MacBookPro8,1
          1 2.3 GHz Intel Core i5 CPU: 2 cores
          4 GB RAM
Video Information:
          Intel HD Graphics 3000 - VRAM: 384 MB
System Software:
          OS X 10.9.1 (13B42) - Uptime: 2 days 3:4:35
Disk Information:
          Hitachi HTS545032B9A302 disk0 : (320.07 GB)
                    EFI (disk0s1) <not mounted>: 209.7 MB
                    disk0s2 (disk0s2) <not mounted>: 319.21 GB
                    Recovery HD (disk0s3) <not mounted>: 650 MB
          MATSHITADVD-R   UJ-898 disk2 : (8.09 GB)
USB Information:
          Apple Inc. FaceTime HD Camera (Built-in)
          Apple, Inc. Keyboard Hub
                    Apple, Inc Apple Keyboard
          Apple Inc. Apple Internal Keyboard / Trackpad
          Apple Inc. BRCM2070 Hub
                    Apple Inc. Bluetooth USB Host Controller
          Apple Inc. iPhone
          Apple Computer, Inc. IR Receiver
FireWire Information:
Thunderbolt Information:
          Apple Inc. thunderbolt_bus
Kernel Extensions:
Problem System Launch Daemons:
Problem System Launch Agents:
Launch Daemons:
          [System] com.adobe.fpsaud.plist 3rd-Party support link
          [System] com.microsoft.office.licensing.helper.plist 3rd-Party support link
          [System] com.oracle.java.Helper-Tool.plist 3rd-Party support link
          [System] com.robohippo.HippoConnectDaemon.plist 3rd-Party support link
          [System] com.trusteer.rooks.rooksd.plist 3rd-Party support link
          [System] cx.pow.firewall.plist 3rd-Party support link
Launch Agents:
          [System] com.oracle.java.Java-Updater.plist 3rd-Party support link
          [System] com.robohippo.HippoConnectAgent.plist 3rd-Party support link
          [System] com.trusteer.rapport.rapportd.plist 3rd-Party support link
User Launch Agents:
          [not loaded] com.google.keystone.agent.plist 3rd-Party support link
          [not loaded] com.spotify.webhelper.plist 3rd-Party support link
          [not loaded] cx.pow.powd.plist 3rd-Party support link
User Login Items:
          iTunesHelper
Internet Plug-ins:
          FlashPlayer-10.6: Version: 12.0.0.38 - SDK 10.6 3rd-Party support link
          QuickTime Plugin: Version: 7.7.3
          Flash Player: Version: 12.0.0.38 - SDK 10.6 3rd-Party support link
          Default Browser: Version: 537 - SDK 10.9
          SharePointBrowserPlugin: Version: 14.3.9 - SDK 10.6 3rd-Party support link
          Silverlight: Version: 5.1.20913.0 - SDK 10.6 3rd-Party support link
          JavaAppletPlugin: Version: Java 7 Update 51 3rd-Party support link
Audio Plug-ins:
          BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9
          AirPlay: Version: 1.9 - SDK 10.9
          AppleAVBAudio: Version: 2.0.0 - SDK 10.9
          iSightAudio: Version: 7.7.3 - SDK 10.9
3rd Party Preference Panes:
          Flash Player  3rd-Party support link
          Java  3rd-Party support link
          Trusteer Endpoint Protection  3rd-Party support link
Bad Fonts:
          None
Old Applications:
          /Library/Application Support/Microsoft/MERP2.0
                    Microsoft Error Reporting:          Version: 2.2.9 - SDK 10.4 3rd-Party support link
                    Microsoft Ship Asserts:          Version: 1.1.4 - SDK 10.4 3rd-Party support link
          Solver:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    /Applications/Microsoft Office 2011/Office/Add-Ins/Solver.app
          SLLauncher:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    /Library/Application Support/Microsoft/Silverlight/OutOfBrowser/SLLauncher.app
          /Applications/Microsoft Office 2011/Office
                    Microsoft Graph:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Database Utility:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Office Reminders:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Upload Center:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    My Day:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    SyncServicesAgent:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Open XML for Excel:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Alerts Daemon:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Database Daemon:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Chart Converter:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Clip Gallery:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
          Epson Printer Utility 4:          Version: 9.17 - SDK 10.5 3rd-Party support link
                    /Library/Printers/EPSON/InkjetPrinter2/Utility/UT4/Epson Printer Utility 4.app
          /Applications/Microsoft Office 2011
                    Microsoft PowerPoint:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Excel:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Outlook:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Word:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    Microsoft Document Connection:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
          Microsoft Language Register:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                    /Applications/Microsoft Office 2011/Additional Tools/Microsoft Language Register/Microsoft Language Register.app
          Microsoft AutoUpdate:          Version: 2.3.6 - SDK 10.4 3rd-Party support link
                    /Library/Application Support/Microsoft/MAU2.0/Microsoft AutoUpdate.app
          Smultron:          Version: 3.8.4 - SDK 10.0 3rd-Party support link
Time Machine:
          Auto backup: YES
          Volumes being backed up:
          Destinations:
                    Time Machine Backups [Local] (Last used)
                    Total size: 412.18 GB
                    Total number of backups: 4
                    Oldest backup: 2014-01-07 12:40:04 +0000
                    Last backup: 2014-01-20 17:50:35 +0000
                    Size of backup disk: Excellent
                              Backup size 412.18 GB > (Disk size 0 B X 3)
          Time Machine details may not be accurate.
          All volumes being backed up may not be listed.
Top Processes by CPU:
              17%          Mail
               8%          mtmd
               5%          mds_stores
               3%          mds
               2%          iTunes
Top Processes by Memory:
          217 MB          Mail
          184 MB          com.apple.WebKit.WebContent
          139 MB          softwareupdated
          115 MB          mds_stores
          106 MB          Google Chrome
Virtual Memory Information:
          186 MB          Free RAM
          1.21 GB          Active RAM
          983 MB          Inactive RAM
          1.07 GB          Wired RAM
          7.85 GB          Page-ins
          326 MB          Page-outs

Answer 1

1. This procedure is a diagnostic test. It changes nothing, for better or worse, and therefore will not, in itself, solve your problem.
2. If you don't already have a current backup, back up all data before doing anything else. The backup is necessary on general principle, not because of anything in the test procedure. There are ways to back up a computer that isn't fully functional. Ask if you need guidance.
3. Below are instructions to run a UNIX shell script, a type of program. All it does is to gather information about the state of your computer. That information goes nowhere unless you choose to share it on this page. However, you should be cautious about running any kind of program (not just a shell script) at the request of a stranger on a public message board. If you have doubts, search this site for other discussions in which this procedure has been followed without any report of ill effects. If you can't satisfy yourself that the instructions are safe, don't follow them.
Here's a summary of what you need to do: Copy a line of text from this web page into the window of another application. Wait about a minute. Then paste some other text, which will have been copied automatically, back into a reply on this page. The sequence is: copy, paste, wait, paste again. Details follow.
4. You may have started the computer in "safe" mode. Preferably, these steps should be taken in “normal” mode. If the system is now in safe mode and works well enough in normal mode to run the test, restart as usual. If you can only test in safe mode, do that.
5. If you have more than one user, and the one affected by the problem is not an administrator, then please run the test twice: once while logged in as the affected user, and once as an administrator. The results may be different. The user that is created automatically on a new computer when you start it for the first time is an administrator. If you can't log in as an administrator, test as the affected user. Most personal Macs have only one user, and in that case this paragraph doesn’t apply.
6. The script is a single long line, all of which must be selected. You can accomplish this easily by triple-clicking  anywhere in the line. The whole line will highlight, though you may not see all of it in your browser, and you can then copy it. If you try to select the line by dragging across the part you can see, you won't get all of it.
Triple-click anywhere in the line of text below on this page to select it:
PATH=/usr/bin:/bin:/usr/sbin:/sbin; clear; Fb='%s\n\t(%s)\n'; Fm='\n%s:\n\n%s\n'; Fs='\n%s: %s\n'; Fu='user %s%%, system %s%%'; PB="/usr/libexec/PlistBuddy -c Print"; A () { [[ a -eq 0 ]]; }; M () { find -L "$d" -type f | while read f; do file -b "$f" | egrep -q XML\|exec && echo $f; done; }; Pc () { o=`egrep -v '^[[:blank:]]*($|#)' "$2"`; Pm "$1"; }; Pm () { [[ "$o" ]] && o=`sed 's/^ */   /' <<< "$o"` && printf "$Fm" "$1" "$o"; }; Pp () { o=`$PB "$2" | awk -F'= ' \/$3'/{print $2}'`; Pm "$1"; }; Ps () { o=`echo $o`; [[ ! "$o" =~ ^0?$ ]] && printf "$Fs" "$1" "$o"; }; R () { o=; [[ r -eq 0 ]]; }; SP () { system_profiler SP${1}DataType; }; id | grep -qw '80(admin)'; a=$?; A && sudo true; r=$?; t=`date +%s`; clear; { A || echo $'No admin access\n'; A && ! R && echo $'No root access\n'; SP Software | sed '8!d;s/^ *//'; o=`SP Hardware | awk '/Mem/{print $2}'`; o=$((o<4?o:0)); Ps "Memory (GB)"; o=`SP Diagnostics | sed '5,6!d'`; [[ "$o" =~ Pass ]] || Pm "POST"; o=`SP USB | awk '/V.*[(]/{if ($3 !~ /0(5a|a5)c/) print}' | wc -l`; Ps "3rd-party USB devices"; o=`pmset -g therm | sed 's/^.*CP/CP/'`; egrep -q 'No th|pms' <<< "$o" && o=; Pm "Thermal conditions"; o=`pmset -g sysload | grep -v :`; grep -q '= [^GO]' <<< "$o" || o=; Pm "System load advisory"; o=`nvram boot-args | awk '{$1=""; print}'`; Ps "boot-args"; d=(/ ""); D=(System User); for i in 0 1; do o=`cd ${d[$i]}L*/L*/Dia* && ls | awk -F_ '!/ag$/{$NF=a[split($NF,a,".")]; print}' | tail`; Pm "${D[$i]} diagnostics"; done; o=`syslog -F bsd -k Sender kernel -k Message CReq 'GPU |hfs: Ru|I/O e|n Cause: -|NVDA\(|pagin|SATA W|ssert|timed? ?o' | tail -n25 | awk '/:/{$4=""; $5=""; print}'`; Pm "Kernel messages"; o=`df -m / | awk 'NR==2 {print $4}'`; o=$((o<5120?o:0)); Ps "Free space (MiB)"; o=$(($(vm_stat | awk '/eo/{sub("\\.",""); print $2}')/256)); o=$((o>=1024?o:0)); Ps "Pageouts (MiB)"; s=( `sar -u 1 10 | sed '$!d'` ); [[ s[4] -lt 85 ]] && o=`printf "$Fu" ${s[1]} ${s[3]}` || o=; Ps "Total CPU usage" && { s=(`ps acrx -o comm,ruid,%cpu | sed '2!d'`); o=${s[2]}%; Ps "CPU usage by process \"$s\" with UID ${s[1]}"; }; s=(`top -R -l1 -n1 -o prt -stats command,uid,prt | sed '$!d'`); s[2]=${s[2]%[+-]}; o=$((s[2]>=25000?s[2]:0)); Ps "Mach ports used by process \"$s\" with UID ${s[1]}"; o=`kextstat -kl | grep -v com\\.apple | cut -c53- | cut -d\< -f1`; Pm "Loaded extrinsic kernel extensions"; R && o=`sudo launchctl list | sed 1d | awk '!/0x|com\.(apple|openssh|vix\.cron)|org\.(amav|apac|calendarse|cups|dove|isc|ntp|post[fg]|x)/{print $3}'`; Pm "Extrinsic system jobs"; o=`launchctl list | sed 1d | awk '!/0x|com\.apple|org\.(x|openbsd)|\.[0-9]+$/{print $3}'`; Pm "Extrinsic agents"; o=`for d in {/,}L*/Lau*; do M; done | grep -v com\.apple\.CSConfig | while read f; do ID=$($PB\ :Label "$f") || ID="No job label"; printf "$Fb" "$f" "$ID"; done`; Pm "launchd items"; o=`for d in /{S*/,}L*/Star*; do M; done`; Pm "Startup items"; o=`find -L /S*/L*/E* {/,}L*/{A*d,Compon,Ex,In,Keyb,Mail,P*P,Qu,Scripti,Servi,Spo}* -type d -name Contents -prune | while read d; do ID=$($PB\ :CFBundleIdentifier "$d/Info.plist") || ID="No bundle ID"; egrep -qv "^com\.apple\.[^x]|Accusys|ArcMSR|ATTO|HDPro|HighPoint|driver\.stex|hp-fax|\.hpio|JMicron|microsoft\.MDI|print|SoftRAID" <<< $ID && printf "$Fb" "${d%/Contents}" "$ID"; done`; Pm "Extrinsic loadable bundles"; o=`find -L /u*/{,*/}lib -type f | while read f; do file -b "$f" | grep -qw shared && ! codesign -v "$f" && echo $f; done`; Pm "Unsigned shared libraries"; o=`launchctl getenv DYLD_INSERT_LIBRARIES`; Pm "Inserted libraries"; o=`find -L {,/u*/lo*}/e*/periodic -type f -mtime -10d`; Pm "Modified periodic scripts"; o=`scutil --proxy | grep Prox`; Pm "Proxies"; o=`scutil --dns | awk '/r\[0\] /{if ($NF !~ /^1(0|72\.(1[6-9]|2[0-9]|3[0-1])|92\.168)\./) print $NF; exit}'`; Ps "DNS"; R && o=`sudo profiles -P | grep : | wc -l`; Ps "Profiles"; for f in fstab sysctl.conf crontab launchd.conf; do Pc $f /etc/$f; done; Pc "hosts" <(grep -v 'host *$' /etc/hosts); Pc "User launchd" ~/.launchd*; R && Pc "Root crontab" <(sudo crontab -l); Pc "User crontab" <(crontab -l); R && o=`sudo defaults read com.apple.loginwindow LoginHook`; Pm "Login hook"; Pp "Global login items" /L*/P*/loginw* Path; Pp "User login items" L*/P*/*loginit* Name; Pp "Safari extensions" L*/Saf*/*/E*.plist Bundle | sed 's/\..*$//;s/-[1-9]$//'; o=`find ~ $TMPDIR.. \( -flags +sappnd,schg,uappnd,uchg -o ! -user $UID -o ! -perm -600 \) | wc -l`; Ps "Restricted user files"; cd; o=`SP Fonts | egrep "Valid: N|Duplicate: Y" | wc -l`; Ps "Font problems"; o=`find L*/{Con,Pref}* -type f ! -size 0 -name *.plist | while read f; do plutil -s "$f" >&- || echo $f; done`; Pm "Bad plists"; d=(Desktop L*/Keyc*); n=(20 7); for i in 0 1; do o=`find "${d[$i]}" -type f -maxdepth 1 | wc -l`; o=$((o<=n[$i]?0:o)); Ps "${d[$i]##*/} files"; done; o=$((`date +%s`-t)); Ps "Elapsed time (s)"; } 2>/dev/null | pbcopy; exit 2>&-
Copy the selected text to the Clipboard by pressing the key combination command-C.
7. Launch the built-in Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.
When you launch Terminal, a text window will open with a line already in it, ending either in a dollar sign ($) or a percent sign (%). If you get the percent sign, enter
exec sh
and press return. You should then get a new line ending in a dollar sign.
Click anywhere in the Terminal window and paste (command-V). The text you pasted should vanish immediately. If it doesn't, press the return key.
If you're logged in as an administrator, you'll be prompted for your login password. Nothing will be displayed when you type it. You will not see the usual dots in place of typed characters. Make sure caps lock is off. Type carefully and then press return. You may get a one-time warning to be careful. If you make three failed attempts to enter the password, the test will run anyway, but it will produce less information. In most cases, the difference is not important.
If you're not logged in as an administrator, you won't be prompted for your password. The test will still run. It just won't do anything that requires administrator rights.
The test may take up to a few minutes to run, depending on how many files you have and the speed of the computer. A computer that's abnormally slow may take longer to run the test. There wiil be nothing in the Terminal window and no indication of progress until it's done. Wait for the line "[Process completed]" to appear. If you don't see it within half an hour or so, the test probably won't complete in a reasonable time. In that case, close the Terminal window and report your results. No harm will be done.
8. When the test is complete, quit Terminal. The results will have been copied to the Clipboard automatically. They are not shown in the Terminal window. Please don't copy anything from there. All you have to do is start a reply to this comment and then paste by pressing command-V again.
If any private information, such as your name or email address, appears in the results, anonymize it before posting. Usually that won't be necessary.
When you post the results, you might see the message, "You have included content in your post that is not permitted." That's because the forum software falsely identifies something in the post as a violation of the terms of use. If that happens, please post the results on Pastebin, then post a link here to the page you created.
Note: This is a public forum, and others may give you advice based on the results of the test. They speak only for themselves, and I don't necessarily agree with them.
Copyright © 2014 Linc Davis. As the sole author of this work, I reserve all rights to it except as provided in the Terms of Use of Apple Support Communities ("ASC"). Readers of ASC may copy it for their own personal use. Neither the whole nor any part may be redistributed.