OOoo-OOOOoo!
I know the answer.
Use as many small batteries as you can cram in there. The more you run in series, the higher your system voltage = the faster your bike goes.
Also, higher voltage means fewer amps for the same amount of work, so it's easier on on batteries and their lifespan. You can also use thinner cabling. High amps need thick cables.
Higher voltage parts tend to cost more. The cut-off points for chargers, controllers, etc, tend to be: up to 48V, up to 72, and above 72.
My cycle goes 45 mph on a 48V system. 72 would be a great system voltage for a cycle, or even higher, if you can afford it.
Use sealed batteries on a motorcycle, as tipping a bike is NOT that hard to do. I had mine tip over once on a trailer when I didn't have it tied down right. Also, vibration is a big issue on cycles. You don't want your batteries getting shaken to death and spilling.
If you haven't read it before, you might want to check out:
http://ecomodder.com/forum/showthrea...rsion-599.html