I run a Micron and Race ECM w/ '07 airbox, K+N and relocated breather vents and don't have any real issues with the fuel map. I just bumped the plugs down to one notch cooler and the OEM plugs looked great.
If it's coughing in the mid-range at around 3000 RPM, that's pretty common even with the stock parts on the 12s.
If I ride mine a bit aggressively, ie: keep the R's above 3200 most of the time, it rarely has a problem with the cough.