I think you people are getting a bit unfriendly and unfair. How do you expect to learn from fixing these types of problems? So we should never use third party apps? The computer is a hobby for me as well as a workhorse.
So lets review what I have done.
Reinstalled Mac OS.
Removed all login items
deleted com.apple.finder.plist
rebuilt the launch services data base
deleted the .ds restore files
repaired permissions
Cleared out all startup items folders.
Zapped the PRAM.
I have multiple hd on my Mac Pro. HD1 is the one with the problems.
I did a clean install of 10.8.4 on another HD called HD2.
I copied over the System extensions folder and the coretypes.bundle folder from HD2 to HD1. Restarted and things look fine. However as soon as I create a new alias or logout and login the problem reappears.
What does work is:
Using a different user account.
Booting in safe mode.