At start-up the Jeep is running in open loop, and all the sensor signals are ignored by the PCM. As soon as possible, the PCM switches over to closed loop, and it starts to adjust fuel/timing/etc based on the signals from all the sensors. You may have a sensor issue, wiring issues to the sensors, something that didn't get hooked up correctly during the swap, or low battery voltage.
For 1996+ Jeeps, the OBD-II engine computer (ECU/PCM) re-boots, and the idle settings are deleted, when you: (1) let the battery run down by leaving the lights or radio on, (2) disconnect the battery for an extended period of time, (3) when the battery goes bad and needs replacing, (4) when the alternator is not properly charging the battery, (5) or when poor battery connections result in a voltage drop at the PCM or poor battery charging. Loose, corroded, or damaged battery cables or ground wires may also cause or contribute to the problem.
Your symptoms are: (1) having difficulties starting the engine without depressing the gas pedal, and (2) the engine will have a low idle and probably stall unless you keep your foot on the gas pedal. (3) The ECU will relearn the idle settings after a short period of driving and the engine will start and idle normally.
Begin with basic trouble shooting of the start and charge systems. Remove, clean, and firmly reconnect all the wires and cables to the battery, starter, and alternator. Look for corroded or damaged cables and replace them as needed. Do the same for the grounding wires from the battery and engine to the Cherokee's frame/body.
If the symptoms reoccur, you need to have your battery and/or the alternator load tested at a repair shop or auto parts store. This is usually a free service they offer to bring in potential customers. Even with low battery voltage, the engine will start, but the ECU can re-boot multiple times and a new battery may be required.
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