Overkill PCM :: Overkill Motorsports ::
Diablo/CMR tunes can't modify the transmission parameters to my knowledge, which is where a big change in how the vehicle drives is made with one of my computer tunes, plus remapping the transmission line pressures and torque management which can make a big difference in the life expectancy of the transmission (stock settings are truely aweful).
For the exhaust, personally I'd get a Hogan downpipe, a ZZP 04" cat-back exhaust and have an exhaust shop modify them to fit together (or if you get a resonator-less cat-back, this is easy to do with one cut).
For intake, the stock airbox actually isn't restrictive aside from the inlet. 20 minutes with a sawzall or other cutting device and a high flow drop-in panel filter would routinely save LS4ers $200 over an aftermarket CAI.