You have been very thorough - when you had the back off, did you check the appearance of the caps? They should be perfectly flat with no exudate.
Since TT showed nothing, try booting from the install disc and run Apple Hardware Test, see what that throws up. You might also want to use
1. Insert the Mac OS X Install disc that came with your computer, then restart the computer while holding the C key.
2. When your computer finishes starting up from the disc, choose Disk Utility from the Installer menu. (In Mac OS X 10.4 or later, you must select your language first.)
Important: Do not click Continue in the first screen of the Installer. If you do, you must restart from the disc again to access Disk Utility.
3. Click the First Aid tab.
4. Click the disclosure triangle to the left of the hard drive icon to display the names of your hard disk volumes and partitions.
5. Select your Mac OS X volume.
6. Click Repair. Disk Utility checks and repairs the disk.
Then reboot from your internal (if you can) and repair permissions.