You can check the coil and Stator with an OHM meter, CDI is more often than not good or bad.
Check the flywheel, too...as said.
Jetting richer than what your motor requires shouldn't be done, it won't get you more power, it will only load the bike up, foul plugs, etc.
The key is to get the right mixture of gas an air to the engine is performing at it's best and most efficient....
Throwing more main jet in will not increase performance unless you're way too lean to begin with, and I don't think you are with FMFs and an airbox still....
The stock air box lid helps hold and seal the air filter to the box. If you remove the lid, the air filter will not seal properly.
The Pro Design plate bolts to the front of the air box and seals, so....you can run NO lid and get a good seal.