To the OP....lot of good info here. I'll throw a little more at you to think about.
No CAI is going to amaze you with the performance gain but in addition to the ones mentioned already you should check into the Vararam.
I would not buy a catback system, especially considering you seem to be planning to redo the entire system anyway. Just pick the muffler you want and have it welded in. Magnaflow, Borla, and Dynomax are probably at the top of the list performance wise but I agree that the performance gain from the muffler alone is minimal at best. If you just love the sound of the Flowmaster, I wouldn't let the performance issue bother you. Another popular header to look at is Pacesetter. They make a killer set of longtubes that are priced great. I would definitely swap the stock y-pipe for something like Magnaflow or I think Pacesetter actually makes a y-pipe of their own.
Depends on how much money you want to drop but the early Hemi engines respond great to cam swaps. Comp cams are popular but I would probably start here if I were looking for one.