My Baja dies or idles down really low after letting up on the gas pedal after warming up at highway speed.

There could be all sorts of problems considering the age of the vehicle from electronic to engine valve seats and only a back to basics approach can fully evaluate the situation - lots of checking and lots of time...

A rough idle could mean a misfire confined to just one or two cylinders or it could be a couple of cylinders that are working but inefficient or it could all be intermittent.

If the car was mine I would begin by removing the injectors and having them checked and if any swarf is found inside it will place a question mark over the high pressure pump.

Should be on or near the fuel injector supply rail.

Low pressure from fuel pump, when the pump is cold the pressure increases, as it warms up the pressure drops (this happens in a pump that is going out) the normal pressure should be at 40 with the key on and engine not running, when started the pressure should stay around 36, any less it won't idle and may run as long as you hold the pedal down. The injectors are opened electronicaly, so as long as there is fuel flow the engine gets fuel to run.So check the fuel pump, soundslike you need a new one

Most likely culprits are the IAC motor, TPS and/or EGR valve. Have them all checked.

Could be several things, a vac leak, dirty throttle body, or faulty idle air control valve.
The computer controls idle speed by how much air enters the throttle body thru the valve.
Usually a vac leak would speed up the engine unless it is causing the rough idle.

The automatic idle speed control system has lost its adaptive idle learning due to the dead battery. To help to correct this in the short term run the engine at 2000 RPM until warm, then back down to 1500 RPM for 3 minutes, then 1000 RPM for 3 minutes, then let it idle for 5 minutes, this should get the system to a point in the idle learn that it doesn't stall out, then drive it for 20 miles under varied conditions of highway and stop and go and low speed operation, that should get all to work again. If you still have problems you will need to have the system scanned to see what is going on that is causing a stall. Also add fresh fuel, gas goes bad in about 3 months. Use the recommended grade of fuel.

Idle air control valve might be broken or pcv valve pipe broken

SCAN FOR CODES THE ONLY WAY TO FIGURE OUT WHATS WRONG
AND KEEPING COST OF REPAIRS DOWN COULD BE TROWING ALL KINDS OF PARTS
AND SENSORS AT IT WHEN NOT KNOWING WHAT THE ECM HASE DETECTED

yes it does if it is reading lets say lower than normal that would explain easy start up and stalling later.the coolant temp sensor has two wires .so if your car warms up and your coolant is about 200 degrees your coolant sensor might say 80 degrees .access to a scanner to check temp would be great.

Have you tryed ajusting your carb choke?