What jets should I run with the airbox lid off and an aftermarket pipe/silencer?
If you want better answers, you need to ask better questions
You're missing a ton of information to even start to think about answering your question.
Porting?
Elevation?
Weather/conditions?
Bore diameter?
What carb are you running?
Type of riding you're doing?
Has the head been modified?
Compression is ??
Does it run now; iIf so what type of gas and what jets are you running?
Is it acting up; if so what's it doing?, what's it sound like?