1987 jeep cherokee pioneer will crank and back fire out of the throttle body, what could it be

Firing order doesn't change on its own and then cause misfires. Did you change something? Most likely cause is spark plugs.

https://www.google.com/search?q=1987+Jeep+Cherokee+2.5l+2x4.+Firing+order

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Check the ignition module, could be in the steering column, could also be a anti theft condition.

You may have a faulty ignition coil. Check to see if system is firing when it won't start. If you have fire it is probably fuel pump.

Extended cranking is the first sign of a fuel problem. Either the fuel pump is now not working or you have a leaking injector, bleeding off pressure. if plugs have wet fuel on them look at injectors. If engine briefly starts when you spray carb cleaner into throttle body look to the pump or filter. Once fuel system has been checked, look for spark. If none, find out why.

my 96 grand cherokee had the same problem with stalling minus the clock reseting part. what fixed mine was an idle air control motor it sits at the back of the throttle body on top of the motor. the part cost about 60 bucks and it hasn't stalled out on me since. i hope this helps you out.

well more questions then answers but a step closer.. good fuel pressure? check the throttle body when someone turns it over. did you try starter fluid ( put on the air cleaner for it, so it dont back fire) anyway if it runs on starting fluid then its fuel delivery system. . Basics three things to run. air, fuel, spark. you have all of these? in good supply? then look to compression and condition of dist. cap and rotor.

Did you have the same cranking with no start problem with original engine or did the problem begin when you changed it? I would check codes if you have not already, and would also clean business end of idle air valve (next to tps) DO NOT turn the end plunger while cleaning or it may not seat properly. Do not loose the rubber "o" ring while working either!

The 1989 Jeep did not come with a Carb it was throttle body injected and the motor should be a 4.0. let us know what motor it is.

You say you changed the cam sensor. A1391 code is a crank sensor on the top of the trans. bell housing.

check your transmission fluid,the motor will stall when fluid is low