Once you start thinking out-of-the-box, you're on your way!!

I'm putting an old Yamaha 400 twin into my chassis. After extending the frame 4" , motor mounts are going to be the second PITA.

Your main focus is chain alignment, intake and exhaust clearance. You can always fabricate an exhaust system from scratch (my twin will be "Y" ed into a single outlet).

Flipping the rear axle (for you) will be a minor mod. Leave the swing arm alone and flip the axle assembly. The sprocket and rear brake assembly will switch positions and require rerouting of brake lines and chain followers.

 

Yeah, just flip the axle around a lot less work, and probably better in the long run. Me and a couple of friends might be doing something like this too, a 2003 Kazuma frame (tranny went) and a 73 Suzuki 185 twin streetbike engine. Good Luck to you