I'd suspect a spark plug before the IAC or a fuel filter. What brand of plugs did you use? Cheap "Bosch" Platinums usually fail at around 10k miles, the center "platinum" tip falls out and they cause a misfire, in my experience! Regular cheap Champions work very well in a 4.0l! I'd stay away from "Trick" plugs in any event! A diagnostic Scope check will tell you right away if it's a plug ot other ignition system problem.

You can eliminate the IAC by simply unplugging it, it will set a code, but it won't be able to move causing any surge.

A bad filter would show up under a heavy load, or with low fuel pressure.

Note: Normal slight fluctuations or change in exhaust tone will occur as the PCM varies the fuel pulse in response to the O2 sensor reading. The PCM wil drive the pulsewidth past the .5 volt switching point, a little rich to heat the cat, a little lean to give the Cat O2. This is normal.

Lastly, Keep that original coil in your console or glovebox as a trail spare, it's the most likely part to fail on you!