As far I as can tell from my reading on this forum, if you have the stock muffler and air cleaner, you will get better performance and less backfiring if you replace the white spacer with one that is half as thick and adjust the idle mixture.
If you add a high flow muffler and a high flow air cleaner or either, then you'll get a lot more air to the combustion chamber. That will cause a lean condition which will increase backfiring and make the engine run hotter. The only solution is to increase the size of the main jet which will add more fuel and "richen" the misture.
I installed a HD Dyna muffler weekend before last. The engine was running very lean and backfiring more.
I did both this weekend for my 97. I found a #4 nylon washer at the hardware store that is exactly half the thickness of the original spacer. I installed that with a 152.5 jet. I also removed the snorkel.
The engine runs much smoother with those mods. Seems to have more power too. I just got back from a short ride. to test it out. As I approached home in second gear, I decided to roll on the throttle to see how it would respond. The front raised up and I thought I was going to pop a wheelie for a second.
So why did you buy a new stock carb?
Steve