When stock, I too was getting low to mid 40s for MPG. If you wish to raise the MPG performance on a stock bike, I believe you'll need to let it breath better than what the factory spec'd. The stock pipes are a major problem in the breathing process, although the quiet of a stock pipe is a great thing on long trips.
Anywho,
I run a year 2005 865 cc Speedmaster and get a nearly constant 50 US MPG on a 10% Ethanol blend of 89 octane gas. Odometer reads 19K. I weigh 250 US lbs, and carry 25 lbs of saddle bag tools & flotsam.
Mods:
Stock pipes gutted to 1 & 1/2 baffles
130 jets
Uni filter with drilled out airbox
Drilled slides
Stock needles
With one hardware store washer for a shim, I ran what one dyno software writer calls 'perfect' which I believe they peg at 13.6 : 1 Air to Fuel ratio. With the above mods & 1 shim, I was running low 40s for MPG.
Since the theoretical optimum Air to Fuel ratio is closer to 14.x : 1, I figure it was safe to lose the 1 shim. It's cooler Autumn New England weather time here, and I ride all Winter when the roads are dry, so running a might leaner as a result of pulling the shim shouldn't (hopefully) equate to any discernible loss of engine life with the colder air and all. With the shim gone, I run a very consistent 50 MPG, (that's with zero high speed 90 MPH type slab miles.) At $3.20 US per gallon for 89 octane fuel, I'm OK with 50 MPG. I expect I'm real close to factory torque & horsepower numbers right there.
If I want to turn it up, some 160 mains and a coupla shims and 40 lbs in the rear tire will push me up to 67 or 68 HP / 30 - 35 MPG. Since I have no income at the moment, and the bike is my primary ride, I'll go with the high MPGs for now. No biggie ... ;-}