Thanks for the suggestion Sten. Jed mentioned a simliar problem with the Dodge Neons. We are moving in the direction of fuel pressure confirmation etc... Bill and I have a few pictures to upload, and will do so very soon.

We worked on the Jeep for a few hours yesterday.
The speedometer wasn't working, and that certainly wouldn't allow the ECU to learn effectively. We fixed that first.
Bill wired a ground strap from the block to the chassis. The car alarm began to function properly afterwards!

Additional ground straps will be wired.
Hopefully, the reverse lights begin to work with the addition of more ground straps. If so, we will wire the rear bumper lights to work in unison.
We will test the MSD ignition coil again after the addition of more ground straps. In the past, the MSD ignition coil caused the ZJ to stall after 10 minutes of driving.
The timing checked out perfectly. We wanted to eliminate this as a possible cause.
I stopped by Auto Zone last night to see if they loaned out any fuel pressure tools. No luck. We will absolutely be checking fuel pressure at the fuel rail. We understood there to be 49 pounds for Mopar, but it's possible the the early ZJ's run at 39 pounds. In the meantime, we will put a couple hundred miles on the motor to allow for the ECU to continue learning.
I swapped the silver 5.9 ZJ louvred hood in place of the stock 5.2 ZJ hood. Eventually, I'll need to paint it black to avoid the perception of being a member of Raider Nation.
The brakes are working good enough, but they should drastically improve with more vaacuum. Eventually hydro-assist will be added, but for now it will probably be a matter of cleaning up the rotors and installing a vaacuum can.
The fuel injector clips/pigtails will all be re-wired at some point.
The cb will be installed soon.
The new 2012 goal for the ZJ is to run Moab and the Rubicon!
John