You'd be surprised how these engines will operate with a broken or breaking-in-progress rod. It has happened to me twice.
Did the engine sound like this:
https://dl.dropboxusercontent.com/u/5447172/jeep-engine.movThat is a video of my second engine with 134k miles, about 5 minutes (of idling time) before the #4 rod cap came off entirely and the bottom of the rod was jammed through the side of the block where the EGR valve had been.
I'm not trying to be doom-and-gloom even though it might feel like it. I'm not confident that this IS a rocker issue, but it COULD be. It is about a 50/50 shot. The good news is that the rockers are the designed failure point, so they ARE the weak point in the engine. Also, the resulting combustion with broken rockers can be *VERY* unhappy sounding, or not as bad. You could have the bad version. The only way to be certain is to pull the top off and look at the rockers.
You don't need to worry about the timing or pins if you are going to disassemble the engine to the rockers and have a look - the timing can be reset easily with the valve cover off, and you won't hurt anything at all. How confident are you working on cars? I will be going to Greensboro in the next few days, so if you pull the valve cover and find the rockers bad, I can build it back up from that point and you are back and running this week.
This would also be a good time to think about the ARP studs and the intake elbow if you haven't done either of those, since the labor is the same for the studs and the rockers - but I would pull the engine apart before ordering anything, just in case it IS the bottom end, you haven't bought anything that you didn't need yet.
Send me a PM and we can discuss your options.