Back-fire could be a few things, most ignition related than anything, plug wires, coil, do you have any codes (engine light) on. Many people need to get away from these canned tunes, example I had a customer come in with a 96 he had a blower installed on, he wanted us to tune it. After data logging the car, it was out of fuel, out of spark and the maf pegged yet it ran okay, there is a example of a car if the customer would have made a pass on his mail tune, boom he would have needed a shovel to clean up the mess, however in your case it sounds like a mechanical issue not tune related but more ignition related.