Probably your hard drive. The CPU was overworked in reading it. Hope you have backups. If you can start with a new drive you may be able to transfer files from the old drive.
First step should be to try booting to your installation CD. If that works you probably have bad sectors in you operating system. Repair option might work. A more thorough job would be to run CHKDSK to see how many bad sectors there are. I would advise against having anything repaired automatically if you value the data.
I pulled the primary HD and tested it in another pc. Appears to be fine. HD is not the issue.
Perhaps reset of core voltage or somesuch.
The only other likely sources of clicking would be the PS fan or graphics card that seems associated with your problem. The thermal paste under the CPU can harden after prolonged use so it could be replaced. If the system won't start with the system disk then maybe the CPU fan is a problem.
It's a good idea to make note of what your system settings were BEFORE you pull the CMOS battery or reset the System Settings back to their Defaults.
Have you tried pulling the CMOS Battery for a few minutes then inserting a new one and Resetting the board to System Defaults? If you have a spare hard drive around I'd stick that one in just for testing purposes. Make sure you have no External Drives hooked to the machine and disconnect anything internal that may affect the System Default board settings. If you've run CHKDSK /F /R on the old drive via another machine there is no reason to believe it won't boot up on the original machine providing the processor isn't cooked (Which I Doubt Seriously).
Troubleshooting means getting back to basics then adding things until you get to the one that fails. Most of the time everything works out just fine. When I get into a situation I leave nothing to chance. I mean pulling all the cards and blowing out the bus and cleaning the card, pulling all the memory and reseating all cards and memory so there is no stone left unturned when it comes to tracking down what could be a needle in a haystack.
Write back if things don't go quite right.
When booting to the install, recovery disk or other bootable media some temporary files are written to the hard drive. It may not be a safe assumption either way about the hard drive as a problem without running CHKDSK. The short memory test available at boot would probably find memory problems. The CMOS and component reseat approaches are the fastest ways to find problems. Multiple restarts are often required.
The new paste used by Intel for fans seems to be good but reviews of similar products on NewEgg suggest they differ.
Wanted to echo that it's probably a good thing to try clearing the CMOS - it's possible that an error event such as that triggers a critical failsafe mode to prevent the system from remaining on, and the only way to get by that is by clearing the BIOS.
I'm assuming you replaced the thermal paste when you replaced the fan, but if you didn't I would definitely check that, as well as ensuring that the heatsink mount is secure to the board. After years of vibration, things can work loose (I had a Zalman heatsink that, after a year, managed to get a bit loose and was causing the system to constantly throttle).