I just put a 250 top end on a 2008 200 and am getting a POP/ POP/ POP when chopping the throttle. It is sort of like knock but I'm not sure what to make of it or what it is telling me. I think a small or occasional amount of this is quite normal on most bikes. Are 250 Betas more prone to this? Raising the needle to full rich helped but some of it is still there. Otherwise it runs OK. The plug looks OK. Starting and idling are good.

This Mikuni has a 5C23 needle, 2.0 slide, 145 main and 30 pilot. Is the 250 needle or slide different? There is also a 66 stamped in the carb body on the engine side.

Sounds like you may have an air leak. Have you checked everything on the intake side and the exhaust is sealed to the barrel properly etc? It only needs a tiny bit of air in the wrong place and it will possibly do what you are describing?