Maybe you've got a little water in your tank, and after swishing it around and reinstalling the tank, you might have sucked a small amount of water into the carbs.
I would drain the carb float bowls, if you can, into a glass jar. The water will settle into the bottom of the jar. If you DO find any water, then completely drain the tank by removing the petcock to ensure everything is water free.
I know it sounds bizzare, but I have seen this before, inluding on my buddy's VFR800, which is fuel injected, but suffered a small, intermittant stutter as the small amount of water got sucked up by the pump.