Hey - Don't get discouraged. When we media blasted my Challenger, we found a lot of ugly spots. Mine had primer covering a lot of dents and rust pinholes.
Your roof pinholes can probably be welded up, and the other things you mentioned are available as re-pops (if yours are too damaged to use). A word of advice (and don't take offense if you already know this)...Take a bunch of measurements under the car, and make sure it is straight, before you start any bodywork. I have seen people spend a lot of time/money in bodywork, only to have things not line up, because of previous crash damage.
Chin up - Now you know what you have, and there won't be any surprises! Good luck to you!
-Tom