Oh, I wish I had the answers for you! Truth be told, even though I've been riding on and off for 20+ years (some years more seriously than others), I am a complete noob when it comes to building up a frame. I am totally counting on everyone here, Google, and three LBSs to steer me right. I do think that the 700cs are the same as 29ers, however. If that is the case, the 26inch vs. 700c would make a HUGE difference, as the brakes wouldn't line up right on the rims (well, assuming you are running rim brakes, that is).
Okay, all you experts out there, any more advice?