If you want to do a real clean install of win os such as win xp, then go to your hard drive mfgrs website and download the diagnostic program for your hard drive. Inside the program you will find a "zero write" or "write zeroes to hard drive" command there, use that one. It returns your hard drive to its original factory condition, minus the normal wear you have put on it.
One thing, when i mentioned you can get a virus without being connected to the net, i should have pointed out that the worst of virus\malware\trojans, etc, will affect your mbr. The "zero write" program also repairs your mbr.
This prevents any such problems from affecting your os when you install it. I do this for all hard drives before installing windows.
so you may want to do this and then install your os afterward, since you have just installed your os you likely dont have much on it so it wont be so much work to get back where you were.
And the fact that you have cleaned your hd in windows but still have these issues leads me to think you might have a mbr issue anyway.
Or, you may have installed a prog that accesses your hard drive when you arent aware of it.
Do the ctrl\alt\del to get to task mgr\processes and have a look under cpu and see what is using up your cpu.