Your Indy may be 100% right but this is my take on your popping...
I found it very difficult to install the header pipes "as a pair", keeping them aligned to the cylinder heads and support brackets,,, allowing EACH to seek their own position,, tightening down the flanges and having no leaks. That's a tall order. It's easy to do with independent drag pipes but as a welded pair I found it tricky. I took my time with new header gaskets and would have bet a grand I had no leaks but I did have a rear cylinder leak on the first & second go around. They were small leaks but they were there and I had popping.
I was able to borrow a friends EVAP smoke machine (used to find leaks on automotive EVAP systems) and nailed the leak in minutes. I also used Walker high temp acoustic sealant on the wire mesh gaskets and slip on's. Yes, it makes it hard to remove them if you need to but I did not care. I wanted absolutely no leaks from the piston to the exhaust tip.
Before you jump into the maps, you may want to check around at a few local automotive repair centers to see if one of them has a smoke machine. Just jack the bike up and remove both spark plugs. Using a plastic straw, place the cylinder you want to check on the exhaust stroke. Pump the smoke into the spark plug hole (not the exhaust pipe) until the smoke comes out the pipes. Now jam a rag in the exhaust slip on's. You will locate the smallest leak in seconds.
It took 3 attempts to finally get it completely sealed for me. I am glad that I did not jump into the maps in order to correct it. It just would have compounded the problem.
If you do "smoke it",, I would like to know what you find. I put $10 on you having a leak,,especially since your header pipes are joined together and must be installed as one..