2001 ninja zx6 idle problems

I recently did some upgrades to my 01 zx6.  it has 12k on it and i put a vance and hines full exhaust, dynojeted the carbs, and put a k&n air filter in it.  at highway speeds its fine but once the bike is hot it wont idle.  it seems to be running on only 2 or 3 cylinders.  i thought it was the carbs but I cleaned them and it is definitely getting fuel. any ideas?  

Problems idling when the bike gets hot usually indicates an overly rich idle mixture. When you installed the Dynojet kit, did you drill out the plugs for the idle air mixture screws? Those need to be set properly, although ensuring the carbs are synchronized would be a good start before attempting to adjust the idle air mixture screws. The idle air mixture screws (sometimes referred to as "air bleed" screws) control and allow air flow into the idle circuit for proper idle mixture.

Adjusting the idle via the idle adjustment screw only controls the throttle plates, making it very rough and imperfect when you're trying to make fine adjustments. This is because the engine causes major vacuum fluctuations at the gap around the throttle plates, due to the surface area involved.  

yeah i had to drill out the plug to screw out the idle mixture screw. it was turned out 1 3/4 stock and now its at 3 which is what the kit called for.  i put the carbsticks on it when i put it all back together and the carbs are synched.  

3 turns out is the starting point. As long as all the other parts and adjustments are correct and in place, you'll need to make adjustments to each carb's idle air mixture screw to maintain a smooth idle. With the engine warm, you'll need to open up the idle adjustment screw just enough to gain a near-stable idle, then adjust each idle air mixture until idle smooths out.