Re: Chain and alignment questions...
I enjoyed that "story" and you made me laugh when I read that part about the sprocket. Don't feel bad, I think everyone has their little stories when it comes to these kits. I had my sprocket on and off 4 times and as far as I'm concerned, putting that sprocket on the wheel is the worst part of putting this kit together.
As for your chain, If everything is "normal" with your kit, I'd say it is impossible for your chain to rub the rear motor mount. The chain is so close to the sprocket that the chain would have a hard time moving sideways.
I'd have a look at the rear wheel, including spinning the wheel and watching the sprocket for an "out of round" situation.
I don't have my bike any longer but I seem to remember about at least an inch of space from my frame . Post some pics on that site, if you can.
edit; Oh I see you posted a pic