Have you gone into keyclone and set the max background frames per second? The slave windows shouldn't need more than a max of 15 FPS and it should help stabalize the framerate on the main window.

Also, turning the graphics way down in the slaves should help. Kill sound and shadows, as those can eat up a lot of resources.

Aero in Vista is a source for contention. Personally, my games ran like crap with Aero off, however, other people saw great increases with WoW when they disabled Aero.

Mods can also be a drain on the system. Questhelper was notorius for a while for it for some people.

Are you Symlinked, running from one folder or multiple folders? That can impact your performance. I can't walk you through that as I've never symlinked, but you should be able to search for it and find a few nice walkthroughs here.

Edit - also, never underestimate the power of a good clean and defrag.