0% CPU usage / Very Slow

First off, Didnt know which forum to put this in because it's getting to the point where I have no idea what the problem is.

My computer has been getting slower and slower over the last two weeks until now its finally gotten down to pretty much a standstill and even trying to find ways to diagnose it are becomming troublesome because of how slow it is / locks up when doing nearly anything. (about 1 min to even get task manager open).

CPU usage reads from 0% - 5% on average, usually floating at 0. I'm certain its not actually the processor as I've had the chance to try a different one with no change. [ another odd fact is that if I move task manager window around a lot the CPU usage usually goes up from 0% to about 40%ish looking more active ]

I've tried installing Win7 on a new HD via a flash drive (I have no DVD drive..) and after the "windows is loading files" screen it pretty much freezes there, killing that plan.

A memory diagnostic revealed no errors there.

I've used CCleaner in particular to get rid of Index.dat files, no help.

I'm thinking its possible its a motherboard issue (I'm surprised its lasted as long as it has anyway) - does that theory hold any water? (FSB having trouble communicating with CPU or something?)

Also possibly still the HD - whats another way I could try and get win7 installed on a new one without a DVD drive? (Or a way to test this problem)

What else can I try / Can it be?