I am new to jeeps but i have been working on cars for some time now. It sounds like you gave the mj a good tune-up ( that will certainly help) but maybe left some things out. Bogging and backfiring is a common problem with emission control problems, they can range from just a simple vacuum leak to faulty Cat. converter. But in your case i would bet it is a vacuum leak of some sort, check your EGR valve!! it is commonly overlooked and they go bad very often and people don't realize it. Look for vacuum leaks around the intake and exhaust, this can cause a bad fuel mixture and backfiring also. Pull out your service manual and got to the trouble shooting guide it can direct you to the right path.