When I installed aftermarket pipes on my bike I had some serious popping issues as well. Both on stock map and on each and every custom map that I had experimented with.
For some reason I have difficultly with Tune Ecu saving settings I guess. For example: after removing secondary butterflies, shafts, and motor, the bike responds with a FI error code as it should. Through Tune Ecu, it was my understanding that I could remove any error codes and I attempted to do so by checking the box, however the FI error is still present and still flashes. If you have the SAS system still installed, make sure it is saving your settings.
Also, does simply disabling the SAS through Tune Ecu remedy the popping noise? Since all the hardware is still there, and the blanking plates are not installed, perhaps the popping noise is still present because air is still allowed through the hoses. My advice: get a pair of block off plates and yank that junk out of there. This almost completely fixed my popping problem. I still get some pops when ridden hard, but I feel like this will go away once I get a proper dyno tune.