First mod to exhaust was different stages of the drilling process before eventually pulling the baffles. Never saw a mpg drop, always hung around 47 - 49 mpg.
Bought new pipes, added a BAK and FI2000R at same time.
Running stock Cobra settings of 4-2-0, too rich. After several settings, I've been running 2-1-1 for some time and get around 43 - 45 mpg, depending on my wrist control.
I also put on the front overdrive pulley the week before, but hadn't put enough miles on to check mpg before the exhaust/intake mod.
Definite difference in torque, throttle response. I didn't expect to gain performance w/out sacrificing a little economy.
Personally, the trade off is worth the 4-5 mpg hit. The 900 still gets 13 mpg more than my friends who ride a Honda VTX1800, and an HD Road King.