The best kind of disabling security you can do on a vehicle is one that uses several cross over features and tucks in the wiring well.
IF i were to do another system I would use some of the open relay slots in the under hood fuse pannel and do an ignition wire cut to the coil pack/rail and another wire cut on the signal for timing. Two relays that feed into the interior to a central connection point. The third wire cut would be done under the back by the Tcase for the fuel pump and the relay controlling it to be under dash. Keep all of the cuts clean and stock looking for anyone taking a quick glance.
The next part is a little tricky and i haven't finished my research on it, but it would be a solid state control unit that controls the two leads for the 3 relays (2 under hood, one under dash), and requires a magnetic clip lead that has a specified ohm resistance to it. Magnetic lead is on, circuit resistance matches the control units paramater it allows the two leads to be powered up and the jeep can start and run. When you leave, you pop off the magnetic clip and all you see is a set of points. Any nitwit who just runs a jumper wire across them doesn't give the right resistance and you don't start.
Other variants if you are worried that someone would see the control unit and just jump it for power, you could set up the 3 relays to require ground signal to close the circuit, and supplying it with a jumper power will do nothing.