I have a 1991 Jeep Cherokee Limited Edition. Approx. 4 years ago the power door lock in the front passenger side malfunctioned along with the remote button alarm. The jeep would not even attempt to start after that because of the factory alarm malfunctioning. My husband tried to bypass the alarm system through the wiring harness but was unable to do so. Then the jeep just sat for 4 years. I put it in the shop to try to get it up and running again and have put in brand new battery, fuel pump, fuel rail and injectors. They have been able to put the wiring back together and it will start and run but then after 5 minutes or so it dies. They think it's the computer/ECU/ECM getting too hot or something signaling the injectors to shut off. They think I need a new computer/ECM but are not sure....
Running for five minutes sounds like something other than a security system problem (usually shuts off much earlier) but if that has been compromised it needs to be put back together or the trigger wire from the drivers door lock needs to be grounded.
I'd look to the throttle position sensor, map sensor, crank position sensor or the ballast resistor on the drivers fender. You need to do tests on those items as all influence the fuel management system after warm up. Test when it is cold and after it shuts off so you don't mistake a part malfunction only when hot. Hands on testing is the ONLY way to determine accurately exactly what is happening there. Anything else is an educated guess!!!
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