!!Fun!! continues.
I went out and bought a 4TB drive as I realized I could really use the space. Spent the time migrating a ton of stuff from one drive to another, then user data from another drive back to the first one (this'll let me ditch two 500gb drives entirely). Broke the "migrate user folder" action again (I've had it work the first time exactly once, so I was more than prepared to undo and retry).
This afternoon my user profile got corrupted (huff) and spent 2 hours doing a hard drive verification (no issues). Fine, delete the user account, recreate it, put all my user data over (moving files is fast, copying files is slow). Bleh. I swear it was Windows Update that broke it. I was restarting and logging in just fine until I enabled Windows Update (even though it never installed anything because I set it to "let me chose").
Also discovered some problems in making Windows see my H drive as the default program files directory rather than C (I'd make it the D drive, but I don't feel like re-lettering drives right now), but I worked those out (basically: copy all C:\Program Files ... files over to H:\Program Files). I'll skip this next time, not worth the effort; its annoying to say "no, D drive, not C" every time I install something, but this change only effects half half of all software anyway (and breaks some Windows built-in applications).
Had to uninstall and reinstall a handful of applications as a result, but it's fixed now.
As a side note, I discovered that Microsoft's own website doesn't function at 100% under IE8 (which is the default browser on Windows 7). I actually had to download a few things in Firefox (IE 10 then informed me that it wasn't applicable to my system, wtf) which normally Microsoft's site will turn its nose up at and say "no no no, you must use Internet Explorer."