The Airbox lid is a must anyway... If you want to ride with the factory pipe, it sounds like the pilot circuit is what you're looking to check out. New pipe=new carb settings all over.
The clip position affects holding at half throttle. The problem happens before that point, so I wouldn't mess with your needle clip just yet.
2 adjustable Parts to the pilot circuit: Air screw, and throttle stop (idle screw--black, grippy). The air screw is brass and just below (on 220 I think) the idle screw.
My experience in missing off idle has taught me that it could be too rich OR too lean. Turning the screw IN will richen the pilot circuit. OUT will lean it. With your idle set where it is, durn the screw IN until you hear it starting to sputter. That's when you've gone too rich. If you've gone past 3/4 turns IN to get to that point, turn it out 1/4 from the "sputter" point and try that. Adjust idle if neccesary. If you hit that "sputter" point right away, lean it by 1/4 increments until you get the desired off-idle. Hope that's a start.