Fuel drop out is caused by the air fuel mixture slowing down while traveling in the intake.The inside radius of the intake could cause that.
If the performance now is that same as with the stock carb, its probably not a problem.
The only time the stock muffler is a restriction to be concerend with, is if the spark arrestor screen is clogged. We have gutted them and all it does is make it louder.

Don't waste your time looking for a buttefly smaller than 12.5mm, if you do find one the venturi will be too small.
9.5 -10mm is about right for a GX31, any larger is a waste because the engine can't use it and the vacuum signal in the venturi gets weaker as you go larger.

If you try a straight pipe on the exhaust make the inside match the opening at the exhaust port face and leave the pipe long, paint it with cheap spray on paint, run the engine (without prop) until it burns the paint off the pipe close to the engine, where the paint stops burning off is the shortest you want to cut it.