If you have a stumble from idle when you crack the throttle, you may have a gummed up accelerator pump circuit or a ripped diaphragm. The carbs may not be in sync either, and these things are stupid finnicky with how in sync they need to be.
Your other issue is likely happening because of your jetting. You should not need to change jetting with that exhaust. Put the original mains back in and see how things change. If you have the original Keihin brass, use that.