Yes, pressure and air temp changes do affect the EFI bikes; but the MAP and IAT Sensors should make appropriate adjustments as needed.
Might want to do a few additional VTune rides, and make sure your map is set up properly for VTuning. Temp/pressure differences should be automatically accounted for, and VTune H-D should yield corrections if you've recorded correctly with Data Master.
After warming the bike up, a good recording while idling/slightly increasing the throttle just sitting still will give you an idea if the idle/closed throttle VEs are too rich. Look closely at VTune H-D's results after you've collected the data.
Without seeing your latest map that's loaded in the ECM, kinda hard to guess where your rich at.