First step,, make sure the exhaust flange is SNUG,, thats a source of backfire issues,,
The header to muffler joint,, check it,,
HOW its shut off matters,, let if drop to idle,, completely,

The repeated suggestion that is forthcoming is the harley dyna muffler. Lighter, looks a bit nicer, and most importantly doesn't sound like a beetle-bug chirping down the road.  Sounds more like a real motorcycle but not obnoxious.  In most cases it might not even require re-jetting.  If your 99 hasn't always been in your family, you might open up the carb and verify what jets are in there just so you know.

Also, read up on the white spacer mod and air/mix screw.  Finagling these two can help get rid of that backfire...maybe not 100%, but most of it anyway.