Can someone tell me where the immobilizer is on a TJ Magna......

The control unit is called a BEM. Does much more than an immobiliser.

In front of your right knee in the car, behind the lower dash trim. Rectangular black plastic box.

Actual immobiliser circuit is from an antenna around the front of the ignition lock barrel. Through a 2 pole connector that oftern seems to cause problems, this connector is close to the steering column.
Into the BEM. The BEM then communicates to the ECU.
So if the immobiliser circuit is cactus anywhere you will be able to crank the engine when starting but the injectors will not send fuel in.
Gerry

The immoblizer is in the ECU (not the BEM), it can be turned off using reflashing software and an openport reflashing cable

Guide to turning it off here: http://modifiedmagna.com/viewtopic.php?f=6&t=389 (excuse the crosslinking but I'm not reposting this).

The BEM/ECU are paired so you cannot swap either without either doing both, or reprogramming the ECU.