Unfortunately the R65 is not a good candidate for upgrading the engine, all I've ever heard, is you can pour a lot of money into it, and have a meager increase in power output, and engine longevity suffers because of it.
Personally I would not try to tinker with the engine, now if you have a destroyed engine, I would consider installing an R100 engine .
The transmission, shaft , and final drive are the same as the 1 liter bikes, so you won't cause any problems there.