Hi there Ippeman,
So you have disabled Superfetch, Windows Search and BITS right?
One thing you can do is to just observe Resource Monitor during these spikes and see what is causing this.
Another thing you can do is to just test the drive and see if there is something wrong with it:
http://www.tomshardware.co.uk/forum/282651-32-best-diagnostic-testing-utility
If there is, it may be a good idea to back up the data stored on it.
Sometimes faulty cables could cause similar issues as well. So, it would be nice if you connect the drive with different SATA and power cables.
Cheers,
D_Know_WD