It's possible that you have an air leak too.
If the exhaust is too restrictive, it could be preventing it from running correctly at higher rpm.
You can certainly play with the jetting, but I'm guessing that's not the problem. Stock jetting should be fine with a stock bore carb. If you've made the bore larger, then of course you'll have to increase the jet size proportionally.
Then again, if you made the bore/venturi larger where the butterfly sets, you would likely need a larger butterfly to close the air down to get it to idle correctly.