John Golden of Rolling Thunder gave me a tip a couple of years ago about decel popping, which can be tough with some pipes to resolve completely.
While tune can have a huge impact, if you are sure you have a good tune, often the situation is an air leak at the export port gaskets. Here's a copy of an email he sent me:
HELP FOR DECEL POPPING
Decel popping is usually caused by cold air getting into your exhaust system. It is usually at the heads where the pipes bolt on, but it can be caused by a crack in a cross over or even a loose muffler connection. If your pipes pop when you let off the throttle, and if you don’t like it, you can reduce it or even stop it.
First off, it is only a sound. It won’t hurt anything. It is just fresh air mixing with unburned fuel and exhaust flame and popping off. If you have this problem and don’t like it, you can fix it yourself. First off, with an absolutely COLD engine, try to tighten the nuts at the head. Often you will find them loose and this will reduce or stop the sound. You must always tighten these nuts ONLY when the engine is stone cold. If this doesn’t work for you, it gets a little more complicated.
Remove the exhaust system from the bike. Pull the old gaskets out and replace them with new ones. Now it gets complicated. Reinstall the pipes but only tighten the nuts at the head FINGER TIGHT. Do not put any torque on them at this time. Mount the pipes at the back so that the entire system is on, but at the heads is only finger tight. Now take the wrench and put ¼ turn on all four nuts. Start the bike and let it idle until you can not hold your hand on the head. Shut the bike off and walk away from it until it is stone cold. This means ALL DAY OR ALL NIGHT depending on when you are doing this. Next, put one more ¼ turn on all four nuts at the head and start the bike the second time. Let it idle until it is too hot to touch and shut if off and walk away until it is stone cold again. This means ALL DAY OR ALL NIGHT again. Now come back and put the last ¼ turn on the nuts at the head and you are done. If you have no other cracks in your exhaust system, it will not pop when you let off the gas.
The reason for this technique is that the aluminum head and the steel pipe will expand and contract at two different rates. The first time you install a set of pipes with new gaskets you will end up with a slight gap leak at the head. If you have already crunched the gasket, you have nothing left to take up. By taking it up in small increments you can eliminate the leak.