I ran my S2R with the same Arrow pipes as yours (baffles in) and an open airbox. Initially I ran it with the standard ECU but managed to get a race ECU. Most of my riding was below 5k rpm and I always got around 50 mpg.
I then fitted a PC III and had a custom map, which smoothed out the power right through the range.
This was the final dyno chart (note it also had a 1089 cc big bore kit so won't be directly comparable with yours).
I don't think your race ECU should be so rich - perhaps it's been 'tuned' already.
Avanti Race Parts might be able to read it and download the correct race map, if necessary. Or you could just get Neil at Cornerspeed to do a Rexxer reflash, which might be your best bet.