I had all sorts of problems with my engine when I had the rear-most bolt on my exhaust manifold shear off and cause a minor exhaust leak. I had a hard time finding this exhaust manifold problem and it took a bunch of mechanics observing and one putting weight on the intake manifold to finally diagnose the leak. It never crossed my mind that the exhaust could be the cause of the engine's operating trouble, emissions difficulties.
I don't want to knock the PaceSetter Exhaust (course 1 or 2 of those have been known to leak), but if their are leaks anywhere from the manifold/header on back, that might be causing you a backfire problem. It might also be caused by a leak on the intake side of the equation, but that's probably less likely and probably easy to spot, too.
If the fuel filter doesn't do it (and I kind of doubt it will) maybe check out the exhaust, get a friend to lean on the intake manifold, do the soap bubble and water deal. Good luck.