For maximum MPG, I'd work extensively on aerodynamics. I think motorcycles have Cd's from 0.5 - 1.0+, depending on rider position and installed fairings. With highly developed fairings, 125cc is all you'd need, but the United States is allergic to small bikes.
If you ever do engine work, I'd consider stroking it to increase low-end torque. The nice thing about small bikes is they are cheap to own and work on.
One thing that would be smart, but no one ever uses anymore, is a chain case. Chains and sprockets are probably the biggest mechanical consumables on the bike, why not protect them?
Chain Case
Some more extensive fairing ideas that could be made at home are the dolphin and dustbin types. Craig Vetter's competition saw an extension of the dustbin fairing into a full capsule.
Dolphin Fairing: Honda RC-143
Dustbin: 1958 Moto Guzzi V8
Vetter Full Fairing
I'm under the impression that engine vacuum won't work on low-cylinder count engines (i.e. anything under 3 cylinders) due to the pulses you've described. I believe that is why most small, fuel-injected motorcycles use the alpha-n speed density table to calculate fuel use rather then a MAF sensor. Alpha-N does use a MAP sensor, so I may be wrong.
Great thread, by the way.
- LostCause