First, have you run chkdsk on the boot drive and let it check for and attempt repair of any bad sectors? If you have some, you could be spending a lot of time in error correction and doing a lot of seeking to alternate sectors. Second, you could look through the system event log to see what errors are shown there. To do that click Start -> Control Panel -> Administrative Tools -> Event Viewer. Once in Event Viewer click on the system log and scroll through the entries looking for those flagged "error" to see if you can find hints as to where the problem could be. I warn you in advance that these logs are very cryptic, so you'll see a lot of things that won't have much meaning to you.

The third thing would be to install an SSD and put Windows on that. I guarantee you that'll speed things up.

Oh yes, one other thing - try unplugging your USB devices. Sometimes Windows can have trouble identifying one device or the other and it can seem to take forever trying and trying and trying to identify it.

Good luck.