Theoretically, the EFI is supposed to have enough lee-way in the mapping to allow the use of a free flow kit, and be able to self-adjust for it.
You might have a fuel flow issue or a clogged injector.
Anyway, the exhaust system you mentioned is being used by a few people here, so I should let them mention how they like it. I have read good comments about it.
The taller sprocket is a tight fit in the case, but I think it can make it. Anyway, it should work okay to lower the rpm range a little at cruising speeds, and if you have some minor mods like you are talking about, it should cope fine with it in terms of acceleration too.
I can't say about the Power Commander, one way or the other. I have not tried it. All I can say is that the very few reports which I have read on this forum leave me feeling like it has not been sorted out yet.
A Power Commander or ECU modification on any bike can have an effect on a single cylinder as much as any other bike. The thing about it is that it can only adjust the mixture and the timing, so all it can do is correct them to be best power range instead of best economy range. The real advantage of a modified ECU or PC comes when the engine is modified to make more power internally, and then the ECU or PC can be adjusted to make the most of those modifications.
There typically is some percentage of power increase available with these types of electronic controllers on a stock bike. At this time, I have no data to tell you exactly how much increase to expect on a UCE Bullet.