The filter is clean and I dont feel like the carbs are dirty or it'd do it all the time.
Which filter is clean?
Like Chrisj said, fuel delivery.
When it's skipping, open your fuel tank cap. Stick a piece of plastic in it (zap strap/stir stick) and close it on it, so that the seal is open to atmosphere. While opening the gas cap, listen for air rushing in.
If no more problem, then you have a kinked fuel tank vent line. Did you have the gas tank off the bike, changing your air filter?