When you say you had the stage one kit installed, did you specifically have the ECM changed or a power commander added. If not that is one of the symptoms!
The first things I think of for backfire on decel is not enough back pressure or too much fuel/air mixture (especially if you are putting on a fireworks display). If you are running without the baffles or cut-down baffles, you might want to try a set of torque cones. If your plugs are black you are running too rich. Did you re-map when you put the pipes and air cleaner on?