Another thing you can do is move everything to one hard drive and use the other HDD to perform a "trial-and-error" process.

1) Install a fresh copy of Windows on it. Install all MANUFACTURER drivers (this is VERY important).
2) Install WoW.
3) Run WoW 5 times. No addons, no tweaking (except for cranking all video settings down), just see if it'll run 5 times.
4) See if it works any better.

Even without capping the framerate, it oughtta run. I'm using one card, and I don't cap my FPS (or maxfpsbk). You have two cards. You should be better off than I am even.

This will determine if your problem is hardware- or software-related. You may not even have to spend a dime to make your computer multiboxable once again.