This is a great idea and I've thought about doing the same thing. A counterbalanced motor would be awesome. The early ones were fitted with the external lighting rotor and this performed like a flywheel weight. It made for a setup with good traction and would be an easy to ride bike for those of us who don't like a hard hitting powerband.
Now that I have a 2011 GG, I still think about a counterbalanced motor. Mine has moderate vibration and is OK offroad. If I did some dual sport riding then the CB motor would be a benefit; however this highlights the major issue.
The real problem as always is the gearbox ratios. They are just not wide enough to have a truely versatile bike. So the CB motor that is most useful at higher RPM is hindered by a not tall enough sixth gear. If you run sprockets that favor road use, then first is not low enough for real nasty trail situations.
While your project is a great idea, I concluded it wasn't worth the effort for me. If you proceed, I'm sure a few of would be interested in the results. You might also consider looking for a quad engine. They are counterbalanced, but I don't know if they are identical to the bike motors. I believe the reverse is just an electric motor that was added, so a quad engine might be the best place to start.
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2011 EC250E
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