Manual or automatic?

I think I've come to a conclusion about which way I'm going to go with the transmission. I want to thank everyone that responded in this thread. You guys helped me make a decision with your responses and experiences.
As of now, I'm going with the AX15 for a few different reasons. First, being that I already have one and the bellhousing, stock clutch and flywheel, and a Hurst shifter. It's a 4wd version, but I have the main shaft and tail housing to convert it to rwd.
Knowing I have to tear down the transmission is what made me think about finding a better ratio set, at least for first gear. I found a complete close ratio set from Speedtek in Australia. The set is $2,500 and shipping is $170.
Jeep AX5 AX15 Close Ratio Uprated 1000nM Transmission Gearset
The reason I think this will work is that is that although mathematically the stock AX15 gears with a 2.76 axle gear would pull like a 904 with 4.10's, it would still have steep RPM drops between shifts. I think the close ratio set with 3.73's would keep the engine in the power band better. Again, this is my opinion after reading different threads about this.
Another big deal breaker is that most aftermarket bellhousings require the use of a 130 tooth flywheel. There are 130 tooth flywheels available the 5.9 Magnum engine with the teeth for the crank position sensor. I have a 5.2 that runs fine. I have thought about putting a 5.9 in the future, but a TKX or a T56 would have required swapping the engine too.
I think I'll get a hydraulic clutch pedal from SST to make things easier. Holley has a couple of different torsion bar reinforcement kits and crossmembers that are not terribly expensive. I can make parts, but having something available that has had the research and development and is proven to work helps with the decision to make versus buy. I'll start a new thread with the conversion once I start it.