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?