Does it sound like this?
https://dl.dropboxusercontent.com/u/5447172/jeep-engine.movI hope not - that is what a rocker problem sounds like. Based on recent events, it could also be the harmonic balancer causing a sound short. Pull the serp belt and try it, if the sound is still there, then pull the crank balancer pulley and give it another try. If the sound is gone - there's your answer.
It is odd that you can only hear it from the inside and not from the outside though, but it could be translating through the driveline and rattling the transmission mount. I had an annoying rattle at that point when driving at low speeds, turns out the rubber transmission mount had failed. Jacking the transmission slightly and wedging a chunk of rubber into the space in that mount can also cure the noise temporarily.