Jimmy,
Besides the basic engine manual, check out some of the other posts. Build tolerences will be a big factor. Getting air & fuel in, and exhaust out, will be a big plus. Pick the other mechanics' brains. Get friendly with your local bike shop mechanics. I'm sure this is stuff you're already doing. Maybe post more specific questions on different parts of the engine that you are building.
Sorry I don't have more specific answers for you. I'm learning myself. My brother is a motorcycle mechanic; and I would be more than happy to pose questions to him. Let me know if I can help.
Best of Luck To You!
Steve