I never came back to post a final update. This swap went very smoothly. I figured mechanically it would be pretty straight forward and it was. After removing the auto trans and all the related brackets underneath to hold the shifter linkage in place, re-installing the new clutch/flywheel and transmission was a snap. I picked up an exterior clutch slave bellhousing and the related components. When I pulled the auto steering column, I then removed the auto brake pedal assembly. Its' easy to swap at that time when the column is out. Re-installed the new clutch and brake pedal arms and then the "new" tilt manual column that I had just rebuilt. With help from Machoheadgames on the little bit of wiring I needed to modify, I was able to setup the reverse lights and create an ignition kill switch with a ground that was left over from the auto harness pigtail. I then just removed the TC relay by the firewall and kept the auto computer.
Jeep fired up on the first crank and runs like it should. Shifts great with the new Novak AX15 and the kill switch works perfectly. You'd never know it wasn't a manual trans jeep from the factory at this point.