Is the prop you had with the engine the Bolly Carbon 36x14? Whether it is or isn't, your first sstep should be finding a smaller prop. Unless the engine will swing the prop at 5000-5200 on the ground, it will not be happy and will probably get warm in the air. I don't have any experience with the carb. that's on this engine, and unfortunately just getting a new one will cost you $300.00 or there about. I would take the carb. apart (very carefully) and clean each diaphragm and circuit.
When you say Johnson header, do you mean Johnson muffler? If you are just running it on a short header, it won't idle very well, but the length of the stacks on the muffler doesn't have a great influence.

What do you have the engine in?

DKjens