As a follow up my own post, although I have only been out for a few hours and through 2 self-tuning sessions, the bike runs great. I have just installed:
SE Auto Tuner with wide band O2 sensors
Vance and Hines Power Duals
HD Stage 2 Torque cam, SE adjustable push rods
S&S Cam plate, oil pump and cam bearing
SE Air cleaner
SE Street Canon slip ons.
Comments on the Auto Tuner install: The length of the front 02 senor wires is just barely a little short. I made it work, but a 6 - 8 inch extension will allow me to run it more neatly along the frame rail. When bolted on the V&H PDs, getting the 18 mm (boy, are they big) sensors past the frame was tricky, but they fit. Have a second set of hands available to minimize the frustration. If using the stock head pipes, be aware that the O2 sensor bungs need to be reamed to 18 mm. My local dealer charges one labor hour, which is considerably cheaper than the tool HD sells.