I'd give Jaxon @ RideOnAdv a call - 817-831-9700. He will talk you through all of it in a no pressure conversation. But, as someone who's bolted on all the above, I can tell you that the bike won't even be recognizable once you get it all done. All of those mods work so well together. I used to think get all those mods, then the flash, but after the GenII flash, I don't really think it deserves to be at the bottom of the list. I'd put it at #1 or #2 right by the headers/PCV + AT.
IMO you still need the PCV + AT even with the flash if you've got headers. Might be fine if you've got the OEM headers, but if I zero'd out the AFR's in the PCV, I still got surging at low RPM's and the acceleration was significantly flatter. After >500 miles, I accepted my first round of trims and am contemplating shutting off the AT at this point, or at least scoping down the % change range it can tweak at any given time. I only had a handful of cells that changed fuel in the double digits, so I was very close right out of the gate. I've found that accepting trim after trim leads to a fuel table that's a mess. Accept trims once or twice. If you are still getting whacky trims after one or two times, your baseline map was garbage to start with.
Anyway, the only place where you might lose a very small amount at the very low end of the power curve is with a slip on, but when you get the motor up in the RPM's a little (can't remember, but I think it starts to pick back up above 4k RPMS) it bumps you back up and power gains come back into play. Still all the aftermarket cans weigh significantly less than the OEM boat anchor, and my Leo doesn't need to be repacked for an exorbitantly long time, so I'm happy.
/endsermon
The quick and dirty is - give Jaxon a call.