So chkdsk has been run on both drives but I just had ANOTHER blue screen.

If you want the dmp I'll post it, but in the mean time here's the message I recieved
CRITICAL STRUCTURE CORRUPTION which was attributed to fltmgr.sys.

Since this thread appears to be marked as solved (And it was for a bit, then it mental again) I might start a new thread in a few days if there is no response. Hope that doesn't bother anyone.