I would download and install PC Wizard 2008. I realize you may have to do this in spurts as the system may freeze at various points. But, once you get this free program installed, you want to run it and then select the Temperatures utility. Go into the Options and make sure the Sensors are setup to update in Realtime. Then, with this program open and running, monitor the temperatures being generated on all the components:
CPU; GPU; HDDs, and anything else that will produce temperature readings from the sensors.
Get the program from here:
CPUID
You may also try pulling out all but one stick of RAM at a time. Run MemTest86+ to test the RAM for any faults.
Memtest86+ - Advanced Memory Diagnostic Tool
While you're inside the case, take a few moments to clean out any dust that may have built up inside. Use canned compressed air to do this and make sure all the fans are cleaned and working properly.
Good luck!