I had a 100% CPU problem on my Windows 7 box last weekend. I used Process Explorer and WinDbg to figure out exactly what it was (a bug in Windows Update). A fix for that particular bug was included in an update rollup, but due to the aforementioned bug, it took nearly 12 hours to apply it, with the fan screaming like a banshee the whole time.

However, you seem to have a disk performance thing, so you probably want to throw some XPerf into the mix (not least because using WinDbg is emphatically not for the beginner or the faint-hearted).

OTOH, my default position with hard disk performance problems these days is simply to replace the disk with an SSD. That one change took the boot time (until usable) on Jen's laptop from 5-10 minutes down to about 10 seconds.