I wrestled with the same questions. I think most would agree that the stock header has to go... at minimum the cat has to be removed, the mufflers have to be at least 4" to fill the hole between the bag extensions and fender and IMHO you should use either the TTS master tune or the SEPST rather than a "piggy back" tuner.
I went with V-H true duals (I like appearance and sound better), Klockwerks Revolver cans (i like the angled billet end caps and tone better), SE Heavy Breather, and SEPST (my tuner was more comfortable and I like that)
Also recommend dyno tune rather than smart tune. A good dyno man(with experience using the tuner software) can maximize power and torque curves down in the RPM range, smooth it out, maximize the air fuel ratio and deal with any driveability issues unique to your bike and setup. Mine Dyno's at 92HP @ 4500RPM, 112TRQ with AFR flatlined around 13.2 to 1. Most of the torque kicks in at about 2300 rpm. The Engine temps went way down, throttle response way better, couldn't be happier.
If you are going to spend the money on exhaust and tuner... budget the additional $200 for the dyno time.