Keep eliminating the mechanical issues affecting the chamber. Unless you've identified a clear difference of valve lift at the rockers. tight pushrods when valve should be closed, or audible valve train noise, its likely not in valve train. Id get the compression test done and also a leakdown. The compression test may show a weaker one, but the leakdown will clearly identify a chamber with sealing issues (hung valve, piston/ring damage).
I'd then pull all of the injectors, inspect/test the cups for cracks. while they are out, have them run on the bench to be sure.
Have you changed the CPS? Was thinking about the backfire and wondered if it was causing intermittent timing issues.