Mac Pro (Late 2013) OSX abnormally slow

Hi,
I'm not sure why but my OSX is running much slower then before, weird thing is I don't even install many softwares in it. Below is the description of the issues I'm facing.
Beach ball frenzy, lots of things ended up with beach balls from switching back and forth between apps (safari and cad). Within app itself, safari freezes occasionally and then whatever I click during that time period (like opening a new tab, links in the page) will suddenly open and this goes on with other apps as well, even finder takes a few seconds to show the content.
Start up time : 14.2 sec
Waiting for shut down menu to appear : 15 secs
Click shut down: forever (monitor goes to sleep after 10 minutes of inactivity, but computer is not turned off)
Previously, whenever software update requires restart, os will just hang and give a grey screen error, this will cause my computer to be in a boot loop where turning off will show the same error as well. Only way I find out is to open in safe boot, apply update and all goes to normal but it seems the problem is not solved cause now my OS just doesn't work properly.
Oddly enough, I got no problem installing Yosemite.
I don't think it's hardware problem cause right now my windows 8 partition is running much faster then OSX. Oh the irony

EtreCheck version: 2.0.5 (90)
Report generated October 19, 2014 at 9:55:08 AM GMT+8
Hardware Information: ℹ️
Mac Pro (Late 2013) (Verified)
Mac Pro - model: MacPro6,1
1 3.7 GHz Quad-Core Intel Xeon E5 CPU: 4-core
12 GB RAM Upgradeable
DIMM1
4 GB DDR3 ECC 1866 MHz ok
DIMM2
4 GB DDR3 ECC 1866 MHz ok
DIMM3
4 GB DDR3 ECC 1866 MHz ok
DIMM4
empty empty empty empty
Bluetooth: Good - Handoff/Airdrop2 supported
Wireless: en2: 802.11 a/b/g/n/ac
Video Information: ℹ️
AMD FirePro D300 - VRAM: 2048 MB
AMD FirePro D300 - VRAM: 2048 MB
DELL U2711 2560 x 1440 @ 59 Hz
System Software: ℹ️
OS X 10.10 (14A389) - Uptime: 0:4:9
Disk Information: ℹ️
APPLE SSD SM0256F disk0 : (251 GB)
S.M.A.R.T. Status: Verified
EFI (disk0s1) <not mounted> : 210 MB
Macintosh HD (disk0s2) / [Startup]: 150.00 GB (39.42 GB free)
Recovery HD (disk0s3) <not mounted> [Recovery]: 650 MB
BOOTCAMP (disk0s4) /Volumes/BOOTCAMP : 100.14 GB (12.33 GB free)
USB Information: ℹ️
Apple Inc. BRCM20702 Hub
Apple Inc. Bluetooth USB Host Controller
SteelSeries Sensei Raw Gaming Mouse
3Dconnexion SpacePilot PRO
Dell Dell USB Keyboard
Generic Ultra Fast Media Reader
Thunderbolt Information: ℹ️
Apple Inc. thunderbolt_bus_2
Apple Inc. thunderbolt_bus_1
Apple Inc. thunderbolt_bus_0
Configuration files: ℹ️
/etc/sysctl.conf - Exists
/etc/hosts - Count: 20
Gatekeeper: ℹ️
Mac App Store and identified developers
Kernel Extensions: ℹ️
/Applications/Capture One 7.app
[not loaded] com.Leaf.driver.LeafFwXDriverMatcher (1.2.0d1) Support
/Applications/DiskWarrior.app
[not loaded] com.alsoft.Preview (4.4) Support
/Library/Extensions
[loaded] com.3dconnexion.driver (10.2.0 - SDK 10.8) Support
/Library/Extensions/3Dconnexion.kext/Contents/PlugIns
[not loaded] com.3dconnexion.virtual.driver (10.2.0) Support
/System/Library/Extensions
[loaded] com.avira.kext.FileAccessControl (1.0.0d1 - SDK 10.9) Support
[not loaded] com.nvidia.CUDA (1.1.0) Support
Startup Items: ℹ️
CUDA: Path: /System/Library/StartupItems/CUDA
Startup items are obsolete and will not work in future versions of OS X
Launch Agents: ℹ️
[loaded] com.avira.antivirus.general.agent.plist Support
[loaded] com.avira.antivirus.ipm.ui.plist Support
[failed] com.avira.antivirus.notifications.agent.plist Support
[loaded] com.avira.antivirus.odscan.default.plist Support
[loaded] com.avira.antivirus.scheduler.agent.plist Support
[running] com.avira.antivirus.systray.plist Support
[loaded] com.avira.antivirus.telemetry.agent.plist Support
[loaded] com.avira.antivirus.update.default.plist Support
[loaded] com.nvidia.CUDASoftwareUpdate.plist Support
Launch Daemons: ℹ️
[loaded] com.adobe.fpsaud.plist Support
[failed] com.avira.antivirus.dbcleaner.plist Support
[failed] com.avira.antivirus.ipm.loader.plist Support
[running] com.avira.helper.watchdox.plist Support
[loaded] com.bombich.ccc.plist Support
[running] com.cleverfiles.cfbackd.plist Support
[running] com.edb.launchd.postgresql-8.4.plist Support
User Launch Agents: ℹ️
[loaded] com.google.keystone.agent.plist Support
[loaded] com.logos.LogosIndexer.plist Support
[running] com.spotify.webhelper.plist Support
User Login Items: ℹ️
SmartDaemon Application (/Library/Application Support/CleverFiles/SmartDaemon.app)
iTunesHelper Application (/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)
Caffeine Application (/Applications/Caffeine.app)
Alfred Application (/Applications/Alfred.app)
CrossOver CD Helper Application (/Applications/CrossOver.app/Contents/Resources/CrossOver CD Helper.app)
3DconnexionHelper Application (/Library/PreferencePanes/3Dconnexion.prefPane/Contents/Resources/3DconnexionHe lper.app)
Cinch Application (/Applications/Cinch.app)
Internet Plug-ins: ℹ️
FlashPlayer-10.6: Version: 15.0.0.189 - SDK 10.6 Support
Flash Player: Version: 15.0.0.189 - SDK 10.6 Support
QuickTime Plugin: Version: 7.7.3
Default Browser: Version: 600 - SDK 10.10
3rd Party Preference Panes: ℹ️
3Dconnexion Support
CUDA Preferences Support
Flash Player Support
FUSE for OS X (OSXFUSE) Support
Time Machine: ℹ️
Time Machine not configured!
Top Processes by CPU: ℹ️
      16% avguard.bin
      3% WindowServer
      1% fontd
      0% syslogd
      0% AppleSpell
Top Processes by Memory: ℹ️
436 MB avguard.bin
245 MB mds_stores
155 MB Safari
129 MB SmartDaemon
116 MB Calendar
Virtual Memory Information: ℹ️
5.70 GB Free RAM
5.21 GB Active RAM
678 MB Inactive RAM
1.29 GB Wired RAM
1.03 GB Page-ins
0 B Page-outs

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