I have had my 04 fat boy for a couple years and it had been popping heavily out the exhaust on deceleration.I took it to the harley doctor and he check the tune and made a tweek and changed spark plugs to HD plugs . It worked pretty good but when I changed plugs it got worse. I recently had the head off to do valve seals and gaskets and had read about setting my plugs so they point to the exhaust valve. I did that and now the popping has stopped almost completely. I believe what popping is left is normal and happens mostly when hot under hard acceleration. Setting the plugs so the open end points to the exhaust valve seems to work. I never would have believed it..

 

Check for an exhaust leak