Sounds like your engine got REALLY hot.
Plastic pieces, electronics, and rubber seals don't like heat.
I hate to say it, but the list of possibilities is extensive.
Jeep aftermarket body parts are easy to come by.
By the sounds of it, anything you do to it will be an improvement.
Go for it....Good project for you. Good learner jeep.
Unless your car got hit by lightning, I doubt the PCM is damaged.
If you're getting "EGR VACUUM REGULAR AND EGR LOW FLOW " then replace the EGR valve, and clean the ports.
Worn out fuel pump, or plugged fuel filter.
I say that because I'vee had to change my pump in my 1991 C2500 after running out of gas.
The gas keeps the pump inside the tank from overheating.
If you run out, or drive around a lot with less than 1/4 tank, it's detrimental to the pump.
Plugged fuel filter?
Below the drivers seat inside the frame rail under the truck.
Faulty fuel pump relay?
Blown fuse?
Both should be on the fire wall behind the engine.
You "think" it over heated??
It could be a whole ship load of things.....
Warped head, blown head gasket, contaminated fuel, dirty air filter, worn injectors, plugged catalytic converter.......
Loose, or corroded battery cable connections.
ADDED:
Oh, it turns over, but won't start.
I didn't read the whole question.
The computer may have gone into "protection mode".
I'm not sure how to reset it though. I'm more of a Chevy guy.
Front= Pads and rotors.
Rear = Shoes and drums.
Pay someone to fix them.
Replace the pads and shoes.
You will need to have the front rotors turned or replaced.
The drums should be fine.
Expect to pay between $400 and $600. for everything.
That's weird.
It may be some security issue. Try the other (spare) key.
Try this to clear the computer:
Turn the key to the ignition on position but don't start it.
Press the gas pedal to the floor three times.
Now turn the key all the way to start it.
Let it idle for thirty seconds or so...