Trouble with motorcycle engines is that they have cam shafts that are designed for high revs, 10,000 rpm or so, a geo metro's 1,000cc engine has plenty of power at 3,000rpm but a 1,000cc motorcycle engine isn't going to have the same kind of power output at that low speed.
if you wanted to do this any way, find a shaft drive engine from a motorcycle like a Honda Goldwing, depending on the year you can find a 1,000cc engine up to a 1,600cc engine and they are tuned to run at slower speeds, have a transmission that can handle the weight of a fully loaded motorcycle with trailer and would be easier to hook up to the drive shaft of the rear axle of the car.
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