Setting the valves and the other stuff you mention should have you purring along soon.
It is possible to put a neutral switch in the trans with the trans in the bike. Remove the rear cross engine mounting stud. The switches that are from dealers these days all leak I think I've read recently. Riders are sealing the switch with epoxy around the area where the wire terminals are. It was discussed sometime in the last week or two. Maybe I can find it.