Since you said it just wont flow on ,,,,,ON,,,,,,,, but will flow on prime, I would be checking that vacuum line first thing, I think you already said you have a new one, be sure everything is attached correctly and its not bent off and closed due to the tuning efforts. The next thing, would be the source of vacuum, which is the number two carb, right,??? Did your tuning do something that would stopper off the source of vac to the petcock. The only thing I think that would do this, is a wide open throttle, but that is a very long shot if youve had the bike running. Is it possible for a diaphragm leak to affect the vacuum to that source????
Here is hoping youve got a kinked off vac line to make it easy for you.
Since no one has mentioned this, except for cliff alluding to it, if this overflow continues, you may want to pull the floats, if they are plastic, check for casting flash on the sides of them, take the flash off with a file. Also, Ive heard of oversized carb bowl gaskets interfering with float operation, it may be best to trim them back with a scissors if there is more than say, a steenth of an inch of overlap into the float bowl area. I do this routinely when having the carbs apart on a new to me bike, but have never actually experienced the problem itself.
Fuel flow when its not supposed to,, is very dangerous, if that bike is kept in an attached garage, woe be to anyone sleeping in the house if it starts leaking and a source of ignition is present.