Is this a 4.0 SOHC or OHV? Seems to be a lot of discussion about alternator problems... kind of irrelevant until the engine is actually running, and we obviously don't have that. Also, if the fuel pump runs, the inertia switch is not your problem.
An engine needs 4 things to start: spark, fuel, compression, and reasonably close timing of all 4. No way did hooking up a jump box cause an internal mechanical failure, so we can pretty safely eliminate compression.
You are sure the fuel pump is running, but it doesn't sound like you've verified whether or not the injectors are pulsing. They need power to them, which you've verified, and they also need to be grounded by the PCM momentarily to actually shoot fuel. The correct test is with a noid light plugged in at the injector connector. It is POSSIBLE, and I stress POSSIBLE, to check for injector pulse with a test light by connecting the clamp to power and probing the PCM-controlled wire at the injector. However, this is not really a 'safe' test to perform as the drivers inside the PCM are not designed to handle the load of a lightbulb and it's possible that you could compound your problems. I remember reading that you sprayed carb cleaner or something at it and didn't get any kind of fire, so I don't think this is where your problem is.
You have pulled one spark plug and verified spark, however, it is possible for these coils to 'partially' die. You can use the easiest wire and plug to check each coil posts output. I suspect this is likely the problem, because of the carb cleaner test you performed. Also, it's not a bad idea to use a true spark tester or an old spark plug with a much wider gap when you are checking spark. It takes quite a bit more coil energy to jump a gap with compression and a fuel charge than to just jump in open air.
What does the 'Theft' light do? I don't remember what a PATS fault disables offhand, but most makes disable fuel when it enters anti-theft to prevent flooding. Does the check engine light come on with just the key on? Also, some of the fuses for the powertrain (ignition hot circuits, mostly) are actually in the interior panel, so make sure you check those as well.