The Pro 1200 would fit with the stock pipe, you would just have to come up with a mounting solution. Also, the polaris triple is a long motor, so you might have to move or replace the tank with a smaller one.
The design of the polaris motor is nice, the only shortcoming for them is getting good aftermarket parts and stock ignition components. IMO, you'd be better off doing a kawi or yamaha, all the r&d is done on those conversions. But, if you like a challenge, go for it!
SM