When I vacuum sync my carbs, I always either plug the open vac line going to 3-4 or reconnect it to one of the unused nipples in the case of the one that activates the petcock (#6 cyl). It takes a little shuffling around of lines, but how can you get anything consistent with open vacuum lines hanging there?
And you might want to check out this thread, about synching the carbs:
"A way to figure out individual cylinder mixtures"
http://www.valkyrieforum.com/bbs/index.php/topic,110548.msg1109280.html#msg1109280