I put the TFI module on my 1999 Ultra and have it set to their recommended settings. The bike runs cooler but the mileage has been knocked down to about 35 mpg city and 30-31 mpg highway. Is that about right?
You can back off on the second pot (accelerator pump function) and it will give you better MPG.
Immediately after I installed my stage one setup with a PCV I noticed that my mileage went from 44 to 36. However now that I've had it for a year the mileage is back up to 43. It wasn't the PCV that killed my fuel mileage so much, it was my right wrist wrapping on the throttle with the new-found power of the stage one. Maybe this is your case also.
Just because I ride it like my Ducati? Could that be it? Could be
Actually, the TFI module lowered the performance a bit instead of increasing it.