JK Jeep Performance Modifications?

I have a Jeep Unlimited, 6-speed Manual -4.10 gear ratio-32” tires, that I have added a True Flow XDI intake to. I am trying to decide on a cat back exhaust, MBRP is my first choice, and a programmer or tuner (Superchip, Unichip, or Diablo). Someone suggested that I might think about getting a throttle body (69mm) from Mopar that is larger than the stock (63mm). What are the pros and cons to changing out the throttle body? A second suggestion was made to change out the stock pulleys and harmonic balancer with a performance set. Do they make these for the 3.8 liter? And, if so, what would be the pros and cons to these? If I do make these modifications, would a programmer be able to take these in to account or would a tuner be more beneficial?

Any comments or suggestions would be appreciated.

Thanks

John