Actually, the FIRST thing to do to try to eliminate the popping is to make absolutely certain there are no air leaks in the exhaust system. Once that has been done and confirmed, then if it still pops you can try adding or subtracting fuel at the throttle setting and rpm where you have the problem. There are different ways to go about it, depending on the tuning system. Look for a decel enleanment setting for instance. I'm not the expert by a long shot, so detailed instructions will have to come from someone else.
When you say the idle is too low, how are you determining that? Do you have a known good tachometer with which to check idle speed, or are you just going by the tach on the bike, or perhaps are you just using the ear method? Idle speed is specified at 980 rpm at normal operating temp. That idle speed should be slightly higher when cold, and it will drop to 900 rpm when the engine temperature gets very high. That was the early version of the Engine Idle Temperature Management System, where they just altered timing and fuel plus lowered rpm when the engine got too hot, and eventually used what they called skip-fire (misfire on purpose). Idle speed is controlled by what is called the IAC, and if the idle doesn't respond as noted above perhaps you will need to do some diagnostics on the IAC.
If all else fails, find a good full time professional tuner (not the Harley dealer). Depending on your location that might require a road trip, but it beats the heck out of dealing with local incompetents.
Jerry