ok, couple of questions:
1st and most important: what's the code that FI light shows (when in neutral, it will blink, count long and short 'blinks')
do you have o2 sensor eliminators?
my bike often gets code 17 or 18, don't remember exactly, but it is listed in the manual as "o2 sensor fault" (ie one long and 7 or 8 short 'blinks')
i unplug the o2 eliminator plug, and there is always some water from wash/rain in there... i blow it out, and all is good till after next rain/wash
have you removed SAS?
if not, tuner had to disable it for proper tuning... they might have messed up something there... most likely a SAS plug, but could be a pinched/clamped SAS hose...
was the bike dynoed with the butt-plugs? you say 'currently baffles out' - were they in or out at the time custom map was made? this makes significant difference - taking plugs out of mine without changing the map made it run like a bag of shyt.
what model/year is your SD?