Matt my 250 has done same thing for around 10 months. Ive chased everything like you have. New primary coil new pick up. Different cdi different coil. Checked all connections. Checked harness. But mine doesnt run right first threw 3rd. I have 400 main in. But I can pull a 450 clean threw 4 th threw 6th. But will not pull it till 4th.. but mine has flashes were it runs right for a pull or to then back to crap. Im pulling motor apart this weekend im going threw everything. If I figure mine out il let you know asap.
This problem is not a mechanical problem, It is a rich condition. You need to investigate WHY it is rich if the jetting is the same as when it use to run good. If you have recently changed reed petals, you may have reed petals that are too thin and are "floating" and producing rich like symptoms. Set the spark plug gap to about .020" If the spark plug gap or stiffer reed petals does not fix the problem, I think that you will find the problem in the list below. The symptoms act like a carburetor that is about 2 to 4 main jet sizes too rich.
1. The main jet you are using may not be the same jet that you used when it ran good. Aftermarket main jets are often miss-marked.
2. Spark arrestor is partially plugged.
3. The inside of the stinger has accumulated enough carbon to change the pipe restriction. An over-restricted pipe will make the engine run rich on the main jet and will need a smaller main jet.
4. Different air filter oils will often require a different main jet.
5. Different brands of fuel will change the optimum main jet size. It is not uncommon for Race gasoline or AV gas to need 1 to 3 main jet leaner than premium pump gas.
6. Temperature affects the main jet size. The main jet will need to be approximately 1 main jet leaner for about every 15 deg increase in intake temperature.
7. A 40% increase in humidity will require about 1 main jet leaner.