Mounting the motor wasn't too bad. I did basically what you're doing and built the frame to fit as close as possible to the engine. This way the mounts were short and it looks allot better. The hardest part was figuring out how to step the chain over from the wide motor to the narrow rear hub. Not sure if you'll have that problem or not.How hard was it to integrate mounts/fittings for the larger engine such, Yamaha XT500....?
Regarding the wheels and tires. I only say this because I went through all the same options as you when planning my build. I figured either go with bicycle scale wheels and tires and have a rad and fun bike to cruise around on or go with motorcycle wheels and tires and have a rad and fun bike that you can actually go fast and be "safe" on. Potholes happen and at 50mph a bicycle rim may or may not hold up. At minimum I would go with Coker tires and Coker rims. I believe the rims come in 36 and 40 hole and they're made for the clincher tires. Nothing wrong with bicycle scale builds but if you're talking 100mph it better be tough. Hope that didn't sound too preachy. Just my opinion.