Really slow disk access

our iMac runs like a dog. I've max'd RAM, cleaned and optimized the hard drive. Configured with two non-admin users (myself & my wife - I need right-click but it drives here crazy), and an admin account. iTunes and iPhoto libraries are shared, and they are stored on an external 500g drive. in addition we have TimeMachine active to a 2tb drive thru. External drives are connected thru the USB hi-Speed bus.
Examples of slow: up to a minute to switch users, 10-20 seconds for a cursor in Spotlight, Safari takes about a minute to get "warmed up".
I decided to do a clean install of Mavericks - all previous updates/upgrades were automated via Apple and/or AppStore.
So I'm creating a redundant backup of folders on the internal drive (everything except movies, music, & photos which are on the 500g and backed up via TimeMachine on the 2tb drive).  in total only 172g to copy to another 1tb drive.
I started last night, but it went to sleep and did not work all night. in total it's been working 4-6hrs last night and 8hrs today. There is still 22hrs to go!
Is there any hope for this machine?
Larry :-)
========

I watch Activity Monitor a lot, CPU never really seems to be stressed, nor the Disk. While I don't know how to read the Memory monitor, "memory presure" is typically stable at about 25%.
The terminal showed 0.0 pages written to the pagefile - taken while only doing back-up and Activity Monitor, no real change now that I'm also in Safari.
EtreCheck results:
Hardware Information:
          iMac (24-inch, Early 2008)
          iMac - model: iMac8,1
          1 2.8 GHz Intel Core 2 Duo CPU: 2 cores
          4 GB RAM
Video Information:
          ATI Radeon HD 2600 Pro - VRAM: 256 MB
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
Startup Items:
          MySQLCOM: Path: /Library/StartupItems/MySQLCOM
System Software:
          OS X 10.9 (13A603) - Uptime: 27 days 2:48:17
Disk Information:
          Hitachi HDP725032GLA380 disk0 : (320.07 GB)
                    EFI (disk0s1) <not mounted>: 209.7 MB
                    Macintosh HD (disk0s2) /: 319.21 GB (124.84 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
USB Information:
          Apple Inc. Built-in iSight
          Western Digital Ext HDD 1021 2 TB
                    disk5s1 (disk5s1) <not mounted>: 32 KB
                    Teri-02 (disk5s3) /Volumes/Teri-02: 2 TB (1.12 TB free)
          Canon MP480 series
          Western Digital My Book 1148 2 TB
                    disk3s1 (disk3s1) <not mounted>: 32 KB
                    2Teri BckUp (disk3s3) /Volumes/2Teri BckUp: 2 TB (1.32 TB free)
          Apple, Inc. Keyboard Hub
                    Apple, Inc Apple Keyboard
          Apple Computer, Inc. IR Receiver
          Apple Inc. BRCM2046 Hub
                    Apple Inc. Bluetooth USB Host Controller
FireWire Information:
          WD Passport III 800mbit - 800mbit max
                    EFI (disk1s1) <not mounted>: 209.7 MB
                    Passport HD (disk1s2) /Volumes/Passport HD: 499.76 GB (100.89 GB free)
Thunderbolt Information:
Kernel Extensions:
Problem System Launch Daemons:
          [failed] com.apple.wdhelper.plist
Problem System Launch Agents:
Launch Daemons:
          [loaded] com.adobe.fpsaud.plist
          [loaded] com.livescribe.PenCommService.plist
          [loaded] com.macpaw.CleanMyMac2.Agent.plist
Launch Agents:
User Launch Agents:
          [loaded] com.google.keystone.agent.plist
          [loaded] com.macpaw.CleanMyMac2Helper.scheduledScan.plist
          [loaded] com.macpaw.CleanMyMac2Helper.trashWatcher.plist
          [loaded] com.valvesoftware.steamclean.plist
User Login Items:
          Dropbox
3rd Party Preference Panes:
          Flash Player
Internet Plug-ins::
          Flip4Mac WMV Plugin: Version: 2.3.3.3
          FlashPlayer-10.6: Version: 11.9.900.170 - SDK 10.6
          QuickTime Plugin: Version: 7.7.3
          Flash Player: Version: 11.9.900.170 - SDK 10.6
          Default Browser: Version: 537 - SDK 10.9
          wkDimdimControl: Version: 1.01
          GarminGpsControl: Version: 4.0.3.0 Release - SDK 10.6
          Silverlight: Version: 5.1.10411.0 - SDK 10.6
          iPhotoPhotocast: Version: 7.0
User Internet Plug-ins::
          CitrixOnlineWebDeploymentPlugin: Version: 1.0.94
Bad Fonts:
          None
Old applications:
          Bluetooth Diagnostics Utility:          Version: 2.3.6 - SDK 10.0
                    /Developer/Applications/Utilities/Bluetooth/Bluetooth Diagnostics Utility.app
          Bluetooth Explorer:          Version: 2.3.6 - SDK 10.0
                    /Developer/Applications/Utilities/Bluetooth/Bluetooth Explorer.app
          BodyMedia SYNC:          Version: 1.0.1 - SDK 10.5
                    /Applications/BodyMedia SYNC.app
          CrashReporterPrefs:          Version: 10.6.3 - SDK 10.0
                    /Developer/Applications/Utilities/CrashReporterPrefs.app
          Dashcode:          Version: 3.0.2 - SDK 10.0
                    /Developer/Applications/Dashcode.app
          IBCarbonSimulator:          Version: 4.0 - SDK 10.0
                    /Developer/Platforms/MacOSX.platform/Developer/Library/Interface Builder/Plug-ins/CarbonPlugin.ibplugin/Contents/Resources/IBCarbonSimulator.app
          IBCocoaSimulator:          Version: 4.0 - SDK 10.0
                    /Developer/Platforms/MacOSX.platform/Developer/Library/Interface Builder/Plug-ins/CocoaPlugin.ibplugin/Contents/Resources/IBCocoaSimulator.app
          Instruments:          Version: 4.0 - SDK 10.0
                    /Developer/Applications/Instruments.app
          Keynote:          Version: 5.3 - SDK 10.5
                    /Applications/iWork '09/Keynote.app
          Livescribe Desktop:          Version: 2.8.3 - SDK 10.5
                    /Applications/LivescribeDesktop.app
          Numbers:          Version: 2.3 - SDK 10.5
                    /Applications/iWork '09/Numbers.app
          OpenGL Driver Monitor:          Version: 1.5 - SDK 10.0
                    /Developer/Applications/Graphics Tools/OpenGL Driver Monitor.app
          OpenGL ES Performance Detective:          Version: 1.0 - SDK 10.0
                    /Developer/Applications/Graphics Tools/OpenGL ES Performance Detective.app
          OpenGL Profiler:          Version: 4.4 - SDK 10.0
                    /Developer/Applications/Graphics Tools/OpenGL Profiler.app
          OpenGL Shader Builder:          Version: 2.1 - SDK 10.0
                    /Developer/Applications/Graphics Tools/OpenGL Shader Builder.app
          PacketLogger:          Version: 2.3.6 - SDK 10.0
                    /Developer/Applications/Utilities/Bluetooth/PacketLogger.app
          Pages:          Version: 4.3 - SDK 10.5
                    /Applications/iWork '09/Pages.app
          Plants vs:          Version: 1.0.40 - SDK 10.5
                    /Applications/Plants vs. Zombies.app
          Quartz Composer:          Version: 4.0 - SDK 10.0
                    /Developer/Applications/Quartz Composer.app
          Quartz Composer Visualizer:          Version: 1.2 - SDK 10.0
                    /Developer/Applications/Graphics Tools/Quartz Composer Visualizer.app
          Quartz Debug:          Version: 4.1 - SDK 10.0
                    /Developer/Applications/Performance Tools/Quartz Debug.app
          SLLauncher:          Version: 1.0 - SDK 10.5
                    /Library/Application Support/Microsoft/Silverlight/OutOfBrowser/SLLauncher.app
          Spin Control:          Version: 0.9.1 - SDK 10.0
                    /Developer/Applications/Performance Tools/Spin Control.app
          Syncrospector:          Version: 5.2 - SDK 10.0
                    /Developer/Applications/Utilities/Syncrospector.app
          USB Prober:          Version: 4.0.0 - SDK 10.0
                    /Developer/Applications/Utilities/USB Prober.app
          Xcode:          Version: 4.0 - SDK 10.0
                    /Developer/Applications/Xcode.app
          Xcode SSH Authentication Agent:          Version: 4.0 - SDK 10.0
                    /Developer/Library/PrivateFrameworks/IDEFoundation.framework/Versions/A/Re sources/Xcode SSH Authentication Agent.app
          Yasu:          Version: 2.8.2 - SDK 10.4
                    /Applications/Utilities/Yasu.app
          YummySoup!:          Version: 2.4 - SDK 10.5
                    /Applications/YummySoup!.app
Time Machine:
          Skip System Files: NO
          Mobile backups: OFF
          Auto backup: YES
          Volumes being backed up:
                    Macintosh HD: Disk size: 297.29 GB Disk used: 181.03 GB
                    Passport HD: Disk size: 465.44 GB Disk used: 371.48 GB
          Destinations:
                    2Teri BckUp [Local] (Last used)
                    Total size: 2 
                    Total number of backups: 64
                    Oldest backup: 2013-08-05 12:04:28 +0000
                    Last backup: 2013-12-28 02:32:06 +0000
                    Size of backup disk: Adequate
                              Backup size 2  > (Disk used 552.50 GB X 3)
          Time Machine details may not be accurate.
          All volumes being backed up may not be listed.
Top Processes by CPU:
               3%          WindowServer
               1%          EtreCheck
               1%          Finder
               1%          Activity Monitor
               0%          sysmond
Top Processes by Memory:
          188 MB          Safari
          160 MB          Locum
          123 MB          mds_stores
          78 MB          Mail
          70 MB          softwareupdated
Virtual Memory Statistics:
          54 MB          Free RAM
          1.25 GB          Active RAM
          1.22 GB          Inactive RAM
          581 MB          Wired RAM
          13.12 GB          Page-ins
          965 MB          Page-outs

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    mattdell 7672M 102163 88 106118 6 38973 3 83155 67 124734 4 207.5 0
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    Last edited by yourealwaysbe (2012-11-11 14:41:24)

    Arf -- i noticed firefox was still laggy last night, and on a (second or third) reboot this morning, things are back to being laggy even without having run firefox...
    I'm not sure where to look, but here's the output of mount if that will be of any use:
    proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
    sys on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
    dev on /dev type devtmpfs (rw,nosuid,relatime,size=1962404k,nr_inodes=490601,mode=755)
    run on /run type tmpfs (rw,nosuid,nodev,relatime,mode=755)
    /dev/sda3 on / type ext4 (rw,relatime,data=ordered)
    securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
    tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
    devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
    tmpfs on /sys/fs/cgroup type tmpfs (rw,nosuid,nodev,noexec,mode=755)
    cgroup on /sys/fs/cgroup/systemd type cgroup (rw,nosuid,nodev,noexec,relatime,release_agent=/usr/lib/systemd/systemd-cgroups-agent,name=systemd)
    cgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)
    cgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpuacct,cpu)
    cgroup on /sys/fs/cgroup/memory type cgroup (rw,nosuid,nodev,noexec,relatime,memory)
    cgroup on /sys/fs/cgroup/devices type cgroup (rw,nosuid,nodev,noexec,relatime,devices)
    cgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)
    cgroup on /sys/fs/cgroup/net_cls type cgroup (rw,nosuid,nodev,noexec,relatime,net_cls)
    cgroup on /sys/fs/cgroup/blkio type cgroup (rw,nosuid,nodev,noexec,relatime,blkio)
    systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=27,pgrp=1,timeout=300,minproto=5,maxproto=5,direct)
    hugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime)
    mqueue on /dev/mqueue type mqueue (rw,relatime)
    binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,relatime)
    debugfs on /sys/kernel/debug type debugfs (rw,relatime)
    tmpfs on /tmp type tmpfs (rw,nosuid,nodev,relatime)
    /dev/sda1 on /boot type ext2 (rw,relatime)
    /dev/sda4 on /home type ext4 (rw,relatime,data=ordered)
    All suggestions appreciated
    edit: also, nothing untoward reported by top (i don't think):
    top - 15:52:02 up 16 min, 0 users, load average: 0.36, 0.41, 0.30
    Tasks: 104 total, 2 running, 102 sleeping, 0 stopped, 0 zombie
    %Cpu(s): 0.1 us, 0.2 sy, 0.0 ni, 99.8 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
    KiB Mem: 3930516 total, 779240 used, 3151276 free, 51616 buffers
    KiB Swap: 2626620 total, 0 used, 2626620 free, 285284 cached
    PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
    1 root 20 0 32552 3432 1924 S 0.0 0.1 0:00.51 systemd
    2 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kthreadd
    3 root 20 0 0 0 0 S 0.0 0.0 0:00.04 ksoftirqd/0
    4 root 20 0 0 0 0 S 0.0 0.0 0:00.14 kworker/0:0
    5 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0H
    7 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/u:0H
    8 root rt 0 0 0 0 S 0.0 0.0 0:00.00 migration/0
    9 root rt 0 0 0 0 S 0.0 0.0 0:00.00 watchdog/0
    10 root rt 0 0 0 0 S 0.0 0.0 0:00.00 migration/1
    The lag tends to occur when first tabbing into a directory.  On the second time
    tabbing through things seem to be fast -- i guess that's cached somewhere.
    editedit: i also tried switching back to initscripts, with no improvement, so i guess systemd is off the hook for the remaining problems
    Last edited by yourealwaysbe (2012-11-11 15:13:57)

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