The fuel filter is in the tank and isn't serviceable. They last pretty much the life of the vehicle. On a low mileage JK I don't think that would be the cause of the symptoms you're describing. If there's a reputable local shop in your area you might want to consider having them take a look at it. Anytime I dealt with a fuel injected vehicle that had some type of backfiring problem when extremely hot, it came down to a fuel pressure issue. Just something to keep in mind. It really could be one of a number of issues. It has to be professionally diagnosed. Trying to diagnose the exact problem on a forum would be an educated guess at best. It sounds like there are also other issues that need to be taken care of that might have to do with the drivetrain.thanks where is the fuel filter on it?
The easiest thing to do is get a cheap vacuum gauge and let him show you how to use it. Or have a shop smoke test your Wrangler.my buddy who is a bmw mechanic says its a vacuum leak the last engine i worked on was a 61 falcon very simple don,t know where to start with a vacuum leak