If you look at a Pilot or a Fl350 the tranny of the stock machine is right behind the motor.
Most bike engines tranny sticks back behind the cylinders a good bit. Nearly ANY bike motor will interfere with the stock tranny on either machine.
This makes for little to no room to mount a spool to where it can feed power to the stock trailing arms of the fl350 or the A-arm setup of the pilot.
I have seen a FL350 with a 600cc street bike engine in it but the ENTIRE rear end has to be revamped. There was a spool out back but it was extended quite a bit to do this. The front was redone as well for suspension and brakes.
The tranny of a fl350 will not handle a lot of power and shifting gears if thats a thought. The Pilot tranny has a slipper built in that will help it last longer.
But by the time you do all the mods you will also need to upgrade the front suspension and the brakes.
Might consider a Girard frame first. IMO it would be easier and far better in the end and LIKELY less work.
http://prosandminirailframes.homestead.com/