Even though I think everyone has covered most of the bases for possible troubleshooting tips, I wanted to throw out an idea or two. Hopefully I won't get to repetitive.
1. Update all of the drivers, for every component in the box. (i.e. sound card, video card, NIC, Chipset, all add-in components) it can't hurt to keep these things updated regardless.
2. Update the firmware for all of your hardware in the box as well. Again, it can't hurt to have the latest and greatest when new programming can give your old hardware a bit of a boost.
3. You talked about coping files over to a new hard drive.. not sure how you went about putting the new drive in, but I recommend installing the OS from scratch, and only loading the bare minimum, including drivers, the benchmarking utility, as well as maybe one graphic intensive game. Then run your tests.
4. I know this might sound ridiculous, and I'm sure you have already looked. but if not, check the event log. Maybe there are some signs in there.. (I know, who uses the event log right?! ya never know
)
5. It might be a motherboard issue, and not a processor issue. Have you looked around the motherboard for any areas that may look burned or charred? Make sure to pay special attention to and around the mobo's capacitors. I've had a machine or two that had bad capacitors and those will always create odd problems that can appear as failed components.
Did you have these problems off the bat? Or had you built the machine and the problems crept up over time?
Best of luck! Let us know if you ever find the culprit.
J