Clean, fresh re-install & back to the same problems !?

  hi guys
  after a spell of LOTS of beach balls & things hanging out of the blue driving me nuts, i decided to re-download M.Lion, make a bootable USB drive, erase Macintosh HD,  i verified/repaired the disk w/ D.Utility & proceeded to re-install Mountain Lion + my iLife apps from the original install DVD that came w/ my iMac ( 27'' late 2009, i7, 16GB RAM ) 
being at a loss pinpointing what was causing the trouble, i ran an Hardware Test ( all good.. ) reset the Pram + SMC...everything short of drowning it w/ WD40 ;-)
  it all went smoothly & once done, i checked for software updates & installed them, restarted the computer & started re-installing the non Apple apps i had but NOT before i checked Roaring Apps for any imcompatibilities w/ M.Lion - because of some doubts, a few WERE left out !
  it's been a couple of days now, at 1st all was well but slowly the ''clunkiness'' came back :
  1 - one minute Safari takes quite a long time to launch, the other it doesn't & just zipps through whatever in a blink of an eye..
  2 - same with Mail
  3 - i downloaded a couple of bigger videos from YouTube ( 1.something up to 2.5GB..) threw then in the Trash selected Secure Empty Trash as i like doing &....it either empties it in a sec OR ( most likely.. ) it hangs for a LOOOONG time before anything happens
  sometimes it goes up to half the progress bar ( or 1/3 or 2/3.. ) & then it just hangs in there - 10, 15, 20 or more minutes
  other times it just DOES NOT budge & i'm forced to re-launch the Finder - if i try to Sec. Empty again sometimes it gives me ''...bla, bla can't empty because X, Y, Z is being used, etc..'' yet as far as i can determine NOTHING is using the file i'm trying to get rid of ?..
   to make sure everything is OK i repaired permissions w/ D.Utility often, re-start, got a few more large videos ( these seem to be the ones that are REALLY difficult to get rid of.. ) trash them, try emptying the Trash &.....AGAIN the same thing !?
   ran a full Onyx ''cycle'' to clean, re-set, re-whatever it is it does & after clicking on empty the Trash i got this message, despite the Trash can being empty :
  & this goes on & on & it's getting REAL OLD, REAL FAST !
  now, i've looked in the Forum & found a few complaints about difficulties emptying Mountain Lion's Trash but after reading many, it didn't look like they are similar cases to mine hence my posting this..
   just out of curiosity, i ''loaded'' the Trash before i started writing this, slected Sec. Empty Trash at exactly 10.51 PM & at 11.37 PM it managed to secure empty about 6.5GB of video files...
before i forget, a message i get a lot when repairing permissions is this : 
Group differs on “Library/Preferences/com.apple.alf.plist”; should be 80; group is 0.   - this one comes up A LOT MORE than anything else...
  the only things i can think of as capable of perhaps ''troubling'' my machineare these :
  1 - the Sideffects thingy ( for colored icons on my Finder windows sidebar.. ) found here - http://macmatrix.blogspot.pt/p/sideeffects.html  but i tried uninstalling it ( AppZapper, etc.. ) repair permissions, re-start, run computer& nothing changed so i installed it again..
  2 - i have set up a Raid1 array w/ D.Utility for Time Machine duty, using 2 Western Digitall My Book USB drives, each w/ 2TB capacity connected via a Logitech powered 4 port Premium USB hub, which were erased, formatted Mac OS Extended (Journaled), the works...
  3 - a couple of FW800 NewerTech Guardian Maximus enclosures connected to my iMac's single FW800 output, each loaded w/ 2 X Western Digital 3TB Caviar Green drives which i have been assured by OWC would work fine ( & did in Lion.. )
  one is for my iTunes Library & the other for all my DVD collection
  4 - a custom Dock made w/ DragThing, which i also un-installed, tried, everything was the same so i re-installed
  among all this upheaval a few things HAVE improved their behavior :
  A - iPhoto now launches almost instantly despite i have a few tens of thousands of large size photos in it !? before it took AGES to launch & to shut down & now it's very zippy, even while editing photos
  B - same w/ Preview - it used to hang endlessly while doing eidts to multiple images for example, now it doesn't
  C - printing & scanning w/ my HP C6180 Photosmart is FLAWLESS - before it could get ''temperamental''
  at this point i have been going around so much trying to troubleshoot what/where/how/etc...i've kindda lost my North so to speak
  i would be EXTREMELY grateful if anyone would be so kind as to drive me through a process of TRYING to determine WHAT is causing this MOST FRUSTRATING behavior
last but not least i ran a full ClamXav scan of the whole computer + external drives : EVERYTHING was OK
  sorry for my VERY long post

that looks good, i've run it & this is the result :
Hardware Information:
          iMac - model: iMac11,1
          1 2.8 GHz Intel Core i7 CPU: 4 cores
          16 GB RAM
System Software:
          OS X 10.8 (12A269) - Uptime: 0 days 8:8
Disk Information:
          ST31000528ASQ disk0 : (1 TB)
                    disk0s1 (disk0s1) <not mounted>: 209.7 MB
                    Macintosh HD (disk0s2) /: 999.21 GB (822.06 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
          OPTIARC DVD RW AD-5680H 
USB Information:
          Apple Inc. iPhone
          Western Digital My Book 1110 2 TB
                    disk3s1 (disk3s1) <not mounted>: 209.7 MB
                    disk3s2 (disk3s2) <not mounted>: 2 TB
                    Boot OS X (disk3s3) <not mounted>: 134.2 MB
          Apple Internal Memory Card Reader
          Apple Inc. BRCM2046 Hub
                    Apple Inc. Bluetooth USB Host Controller
          HP Photosmart C6100 series
          Western Digital  My Book          2 TB
                    disk2s1 (disk2s1) <not mounted>: 209.7 MB
                    disk2s2 (disk2s2) <not mounted>: 2 TB
                    Boot OS X (disk2s3) <not mounted>: 134.2 MB
          APC Back-UPS ES 700 FW:829.D2 .I USB FW:D2 
          Apple Inc. Built-in iSight
          Apple Computer, Inc. IR Receiver
FireWire Information:
          NewerTech GMAX 800mbit - 800mbit max
                    disk1s1 (disk1s1) <not mounted>: 209.7 MB
                    THE MOVIES (disk1s2) /Volumes/THE MOVIES: 3 TB (402.7 GB free)
Kernel Extensions:
          at.obdev.nke.LittleSnitch          Version: 3862
Problem System Launch Daemons:
                 [failed] com.apple.backupd-auto.plist
Problem System Launch Agents:
                 [failed] com.apple.afpstat.plist
Launch Daemons:
                 [loaded] at.obdev.littlesnitchd.plist
                 [loaded] com.adobe.fpsaud.plist
             [not loaded] com.bjango.istatlocaldaemon.plist
Launch Agents:
                 [loaded] at.obdev.LittleSnitchUIAgent.plist
                 [loaded] com.bjango.istatlocal.plist
                 [loaded] net.culater.SIMBL.Agent.plist
User Launch Agents:
User Login Items:
          iTunesHelper
          SIMBL Agent
          PowerboxInjector
          RelaunchFinder
          DragThing
3rd Party Preference Panes:
          Flash Player
          Flip4Mac WMV
          Perian
Internet Plug-ins:
          Flash Player.plugin
          FlashPlayer-10.6.plugin
          Flip4Mac WMV Plugin.plugin
          iPhotoPhotocast.plugin
          JavaAppletPlugin.plugin
          QuickTime Plugin.plugin
          Silverlight.plugin
          SpeedDownload Browser Plugin.plugin
User Internet Plug-ins:
          FolxNetscapePlugIn.plugin
Bad Fonts:
          None
Top Processes:
          431.0 %          HandBrake
          43.2  %          find
          4.5   %          JavaApplicationStub
          3.3   %          WindowServer
          1.8   %          sandboxd
          1.3   %          EtreCheck
          1.2   %          mds
          0.7   %          iStatLocalDaemon
          0.6   %          fontd
          0.3   %          WebProcess
meanwhile the Terminal thing seems to be still looking for but not finding anything or if there was something it would already have found something ? you think i can close it or shall i leave it running for a while longer ?
  & you see, this is what's most disconcerting about my computer's behavior, now for the past hour or so it has been TOTALLY devoid of ''gremlins'' -  just like an electrical problem in a car/motorcycle when you reach your dealer to have it checked it never shows itself kinda thing....ARGGG !!! very infuriating !...LOL...

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