Alright, another day, more ticking. I tried to replicate yesterday. I cranked the Jeep, popped the hood and waited. After about 30 seconds of running, the ticking started kind of faint, but then picked up to its normal volume. This is what it always does. This time I was ready with my wooden dowel. I held it to my hear and the noise is definitely coming from under the valve cover. While I had the stick in my hand and people looking at me like I was nuts, I proceeded to listen to all areas of the engine. The bottom end sounded good, as did the side. Not real sure what I was checking for there, maybe piston slap or something, but it sounded okay too. I also stuck it to the alternator, I have heard people say that they can make a ticking sound.
Once I isolated the noise, I was jamming the stick around in there listening some more, and it stopped. It did not gradually quiet itself down, it just quit instantly. I guess my new theory is a lifter. Its like it takes it a minute to pump up with oil but when it does it pumps right up.