Clean install of windows 7 pro 64bit (and yes, I'm using a video card that I got 2nd hand over a year ago). Stutters occur everywhere, soon as windows boots even with nothing else running. I think it was happening before I even installed drivers, though without audio going it was harder to tell for sure.
At any rate, I've got the older drive unplugged and indexing off, and so far I haven't had any further issues (for about 20 minutes now since boot). So, symptoms resolved, but I would hope that this system can handle having a second hard drive in it. It seems nearly as implausible that a default windows setting was that crippling (okay it actually sounds fairly plausible but I'd like to be sure). Anyway I'll call this concluded in a little bit... stress the box out a bit and see if it comes up again. Thanks for your help so far.