Shut off while driving, engine cranks but no fire?

Ok Fuse 20 5amp, did you try using jumper cables for temporary grounds? You dont need to hook them to battery positive, just use them as large jumper wires to ground the engine block and frame to battery negative.
It looks like Fuse 20- 5amp is "Hot in Start". It looks to send a start signal to the PCM through the Clutch Pedal Switch. You're still in a "Crank no start" condition correct? Have you done a test yet to see if youre missing ignition spark or fuel injector control?
Running the jumper cables to battery negative to the engine block is just a short cut test to potential Grounding issues, The reason Im stressing that test is because the PCM grounds to the engine block, and so does the battery, and ground straps are over looked in many cases. Just looking at them doesnt tell us how much resistance a braided frame to body strap.
You can (diagram 1) see that Fuse 20 wont have power until the clutch pedal is down and the key in the Start/Crank position. Make sure you dont have any broken or corroded wires down at the pedals as well.

The wiring diagrams do show an anti-theft module, are you seeing a constant or flashing security light? I would think you would still see the check engine light as well, But if you have a security light On, it will usually shut off a few seconds after the key goes to the On/Run position. Is that something youre noticing?

The GEM module is basically a body control module, just called something else. Below are the listings on page one (diagram 1, 2) and page two. Showing everything that has an input or output from the GEM.
I would check any connectors under the dash or connectors to the engine compartment fuse box. They're pretty easy to check.
Where else are you missing power?

To your 1st question on the window, yes the GEM controls body functions. This is the 2nd diagram from above, you can see there are a 2 control modules here. Calling a failed module is difficult, but here I would go and check this connector for any corrosion, I can see why its not starting with that fuse blown.

This is the GEM (body control module) is located, with its 4 connectors. They are all labelled and you shouldnt have too much trouble locating it, look for broken or rubbed threw wires down where your feet are. Many times wires will just rub threw after 20 years and they short out. The GEM doesnt look to be in a good location when it comes to water.

So the fuse blew after when you were already testing?

I thought fuse 20 didnt have any power? Or was that just a misunderstanding of when it should be powered up, I know that was a Start only fuse.
I would check for any broken or damaged wires down where the GEM is located. Its a place where we may not noticed water sometimes. Just take the key out before disconnecting components. Use a good flashlight and look into the females pins on the harness side of component connectors. Make sure there are no spread pins or green/white corrosion inside or on any pins. When checking for tight pins, I will use a size smaller than the component has, that way I can be sure they will remain tight when plugged back together. Wiring and connector problems can be very frustrating so go slowly and look for discolored or burnt plastic on any connectors as well.