Hey, I just started school here myself, though I'm a freshman living on campus. I agree, Missoula is a very good town to bike in, and I come from Portland, so my standards are high.
Lots of good shops too, it seems. I've been hanging around Missoula Bicycle Works annoying the guys that work there, but they indulge me
My only minor complaint about the infrastructure here is that the main MUP on the river is unpaved. not a big deal when it's dry, but it might be as it gets wetter. I'll see. If it's an issue there are plenty of roads running parallel to it.
Also, if you're interested in that sort of thing at all, I'd put some off road tires on your cannondale and head up to the Rattlesnake Reacreation Area, if you aven't already. It boraders the wildderness, in which bikes are not allowed, but there are something like 80 miles of trails of all levels of technicality. Best of all, it's less than 4 miles from campus!