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I would say you need to determine what speed and what type of riding you want your design to work best at. That's going to determine what would be the best engine size.
If you want the best mileage for short trips at 45 mph and under, your engine choice will not be the same as it would be if you want to run Interstates at 70 MPH. If you want to run in something like a Vetter Challenge, you are going to need more power than you would for just tooling around on backroads.
I personally wouldn't go below a strong 125cc engine, and probably would lean more towards a 250. There are trade-offs, but a newer F.I. single in the 125 to 250cc range is going to give you some pretty good numbers.
Look at what the 250 Ninjas can get with aero mods and the right rider. That engine is not the best design for mileage, but it still can produce some amazing numbers - and it's not running anywhere near its peak efficiency range.
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