1) yes. Remove it and plug the hole. I would use a brass plug to prevent it from rusting too bad.
2) yes. But it's easier than #1. Remove the pipe from the top of the brass block that connects the hose that goes to the heater core, then remove the brass block from the intake, then insert the pipe you had removed from the top of the block into the hole in the intake. (Then PM me and I will buy that block from you...)
3) There is no vacuum leak there but I do not like open nipples myself. Leave it open or plug it. It's up to you (it makes no difference either way).