hi, Mikebits,
if you have another HDD try to boot from that and check the load on various partitions of your orignal one. you can vacate the C;\ by 50% byshifting the content to D:\ or E:\ . Later, try to defrag the c: .
mean time we can also suspect that lot of dust accumulated in the CPU heatsink, and the thermal shout down might be taking place, and we are likely to confuse it as HDD or load related.
Finally, check whether the machine's RAM is too small. you can reduce many proghrams from startup that eat away the ram by pr-allocation of memory opening all programs as per startup.
i suppose we do this under windows, at 'run' , 'msconfig'
all the best