I agree on that possibility, you are most likely hearing slight backfire. If the wires are worn, the plugs probably are too. When did you last change these items? Make sure to use only Motorcraft or Autolite double platinum plugs, and Motorcraft or Magnacore wires. Technically I believe its possible you're leaning out, but plugs&wires are more likely. Check your fuel filter just in case. How many miles are on your car?
Edit: After rereading your mods, I have to ask, do you have any fuel system upgrades, like injectors or a new fuel pump? It seems to me with those mods you should. How recent is this problem?