I need to know if there is anyone that can help me. I own a 1986 yamaha radian 600 I just bought a 1990 yamaha radian 600. My question is can I swap motors from the 1990 to the 1986 if so what possibly will be the difference between the two if any. I already know that the wiring is different. But what else is different if any.

The only change to the engine was the alternator was changed in position. This is why the wiring would be different. I'm not exactly positive, but I don't think this would stop you from being able to do an engine swap. If my memory serves me right, I believe I got this info from Motorcycle Classics magazine.