I took the stock air filter off my 2000 Suzuki Katana 600 and put a K&N air filter in it, when i accelerate it stalls out a bit before kicking up to speed. a slight lag then go.

Changing to a K&N air filter changes the air/fuel mixture for your bike, and you're probably hitting an overly lean spot before things start to even out. For bikes still running carburetors, which I think you have, you can compensate for this by changing to a slightly larger idle jet. Your main jet is probably fine (it's kicking in after the lag); it's the crossover from idle to main jet that's causing the flat spot.
Talk to your dealership parts counter to get recommendations about jet settings. They may suggest, for example, to keep your existing idle jet and go with a different main jet. Expect to try a couple different setups to find one that works best for your bike and your riding style. I would highly recommend keeping your original jets, though, in case you ever go back to the stock air box.

The old saying is let more air in and you must let more out.If this bike is completely stock and you added k&n some bikes will improve some wont without more upgrades.If this is carburated you will probrobly have to jet it (increase size of jets in carbs).If it is fuel injected you will have to retune with laptop.you might want to start with putting a slip on exhaust if your pipe is stock this will let your engine breath better with the k&n.Some bikes when k&n air filter is installed can get away with putting a slip on pipe on like i said.But some cant.It is pretty much trial and error to you get bike tuned right.Good luck