You don't have to drop the trans for a downpipe, you can loosen the two bolts on the cross-member just before the tail housing and jack the transmission up to give you more room to slide it in and out. I can fit a 4" downpipe in and out with larger 2" up pipes and larger manifolds in the way. RickDLance makes a nice 3" pipe.
Definitley upgrade the tuner!! FOR SURE!! PPE or the new Edge Evo tuner. Either will be SOOOOO much better than the bullydog. You'll think you're driving a completley new truck once you get some quality tuning in it.