I thought the vent comes up on the bottom of the airbox with a baffle over it? Seems like any air that came there would have to go through the filter to get in the carbs.
Yep.
I really don't think that air going through the breather goes directly to the carbs without filtration. Remember, the air filter (I have a K&N) widens at the top of the airbox, which also happens to be its attachment point. The area where the breather tube enters the airbox is almost certainly on the outside of the filter.
I did remove the two screws, and I can push the airbox forward just a bit against the carb boots (good thing they are new and flexible). But I will need a second person pushing from the other side because there is quite a bit of resistance. I hope it will work out. I really don't want to have to remove the carbs over this. Although the bike has been sitting for 2 months; it has a leaking waterpump, a bad petcock, and leaking counterbalancer oil seal, and I just got around to doing all this. With my luck, I'll have to take the carbs out to clean them anyway after all this time.