My iMac is doing fine since the erase and install. I am glad it wasn't the logic board or a SL bug.
Can't put my finger it but I suspect the problem may have had something to do with Spotlight indexing my external drive and messing with the location of files, applications, preferences,etc.
I used to have my spotlight privacy settings to exclude the external drive, but either the upgrade to SL or something along the way somehow reverted that setting.
All this time, I may have inadvertently been launching certain apps and using certain folder and files from the external drive instead of from my iMac.....
Anyway, my two cents, for those experiencing this issue consider trying this:
1. System Preferences => Spotlight / Privacy => exclude external drives/volumes
2. Unmount and disconnect the drive containing the cloned back up
3. Disable preferences syncing with other computers using mobileme, etc so that our changes are not overwritten
4. Use a utility like cocktail or onyx to rebuild the spotlight index, the dock, caches
5. Maybe remove caches and other potentially damaged files (e.g, apple.com.desktop.plist, apple.com.finder.plist, apple.com.spotlight.plist, apple.com.dock.plist, apple.com.dock.db from home/library/preferences)?
Try at your own risk, but I suspect this may have been what what causing the problem in my case.