One major problem you would encounter with brewing your own fuel is BATF regulations.
The reasons that alchohol fuels have 15 percent gasoline is:
a. Safety, because alcohol burns clear gasoline colors the flame.
b. Bureau of alcohol, tobacco, and firearms (BATF) regulations regarding distilling. 15 percent effectively poisons the fuel rendering it unfit for human consumption.
I don't know the actual number of gallons per year you can brew without fed trouble but I think it is around 15. Even then, you may need a tax stamp. You should research the law before proceeding because the fed does not have a sense of humor.
Personnally, I think that it would be a great project and you might want to see about goverment grant dollars to help you out. I am including a link here from my former employer.
During my time with alternative fuels we also had a fleet using compressed natural gas. Again, half the BTUs of gasoline. This would be easier to rig up on a motorcycle but you would need to be located near a refueling station as the pump pressures are 2200 lbs. Don't even think about trying to compress it yourself, way too dangerous.
Here is the link to the hydrogen motorcycle. This looks promising.
I don't recall and couldn't locate the E85 hybrid motorcycle that I read about. A modified Honda generator, some lithium batteries, and an efficient motor would put you in business fairly cheap. Most of the motorcycle testbeds that I have seen have been built around mountain bike components.
If you have access to E85 at the pumps, experimenting with a rat bike could prove interesting. I strongly advise using chemical resistant gloves and barrier creme before handling the fuel. I have several stations in my area that sell it at the pump. One thing to consider when using E85 is the oil dilution problem. Twice the fuel with slow burn speeds = more ring blowby and oil dilution. It requires rings with sealed endgaps, something that wouldn't work well on a large displacement thumper.
I have toyed with building an MPG test mule along the way, though never really persued it. Don Vetter, of Vetter Fairings, held competitions for MPG and one contestant managed 477 MPg.
It would be worth a look at the new breed diesels that run on bio-fuel. That would be a real breeze to rig up on a cycle.
Keep us updated, I'm interested. I just did maintenance and troubleshooting on the test fleets so really can't provide much from an engineering standpoint.