[kaisen]

I'd touch up the rock chips on the metal panels and repaint the plastic front bumper. Once the chips are colored properly, apply a clear 3M bra.

Disturbing the factory finish is a bad idea. It will never match perfectly (trust me), there's the possibility (likelyhood?) that the factory rust protection would be compromised, and you'll always have to explain that the car was painted due to rock chips and not some horrific accident -- and only a few prospective buyers will believe you.

The wheels are easy. The dealer may get better rates than you, so it may be better to negotiate and have them do it. It's probably the same guy anyway, they don't do it in-house.