I'm guessing it's a carb issue. With the ethanol fuel they use by me nowadays if the bike sits for 3+months you get all this green shit in the carb and it really fouls things up. You also might be missing the "balance tube", it is a little black tube that runs between the carbs up by the choke. That said you may also be off on the jetting. Let us know what mods you have and we'll let you know a ballpark for the jetting. Your probably going to have to pull the carbs and sit down with them.
I would probably just synch them by eye and ear, the synch tool is like 50 bucks and it works awesome, but you can get it decent by just looking at it and listening to it(it will run anyway). Also, where are you located?