I was having this same issue and fixed it by migrating my OS partitions from my old 250GB drive to a new 500GB drive. Not only did this alleviate the 100% disk usage which would bottleneck the entire system at random, but it's made Windows as a whole boot and run significantly smoother.
I realise this won't be the answer people want to hear, but it's definitely a troubleshooting step worth considering to confirm that it's actually a Windows issue and not a drive issue. S.M.A.R.T checks and such showed no issues with my previous drive, so it may not be obvious what the culprit is until you try some different hardware.