Probert, I think you might have been neglecting one thing, or maybe I did not understand you correctly, when you wrote "It came stock with a #52.5 pilot jet and I've increased the airflow with the muffler. "
You don't increase airflow with the muffler, you increase airflow with the airfilter.
THINK LIKE THIS: The single cylinder engine is like a bucket. The bucket has a lid (the carb) where we pour in air and water (fuel). The exhaust is a pipe leading the air-fuel mixture out of the engine. The effect is the amount of water-air-mixture that you are able to make pass through the bucket in shortest possible time. Ok, so if you get a more open exhaust, more water will run out IF you put more water in. But if you only pour in more water, not air, there will be a vacuum in the bucket, and the flow will not be the expected.
So, you just can't put on a wider exhaust, and go up a bit in jet-size. You must also increase the flow of air. I think your set-up is ok, IF you replace the stock- airfilter in the airbox with a K&N -filter that fits into the box.
Good luck ! 8)