My best guess is you have a small exhaust leak causing the popping. As the pipes heat up and expand it seals itself off.

As for the hesitation, with the work you have done, you may need a good tune. Maybe just a Stage 1 download to go with the mods. Personally I like the PC's.

 

Thank you

 

+1 with Roadkingron.

It's usually one of two things. Lean condition or leak in the exhaust header pipe. Sometimes both and seeing how you've opened up the air and exhaust, sound like that's the cause.

 

Thank you all for your support

changed the stage one air filter back to the OEM air cleaner so far fix the problem

 

You answered your own question.

By going with OEM air cleaner, you REDUCED air flow to the engine.
Therefore you require less fuel

If you replace with stage 1 air filter, you INCREASE air flow, and you will need to compensate by increasing fuel ratio.

My first suggesstion would help you.

Here's another issue:

When HD did the stage one air filter, I assume they re-mapped your ECM for that filter.

Others need to chime in here to see in you're OK with an OEM air cleaner and stage 1 map.

 

With the OEM air cleaner, he's not getting the true benefit of the Stage I. It's just masking the problem which is either an exhaust leak, or more than likely an improper PCV map/tune.

 

Exhaust leak is always the first thing to check on popping. Did you use new exhaust gaskets when you put on the exhaust? Are you flange nuts tight? IF you have a tuner such as a pcIII did you set the throttle position?