Jeep 4.0 liter 1997 Cherokee

DTC P1391 is "Intermittent loss of Camshaft Position Sensor (CMP) or Crankshaft Position Sensor (CKP)".

So the problem is with the CMP or CKP or the wiring in the circuit.

The Camshaft Position Sensor is located in the distributor on all engines.

Jeep Wrangler DTC P1391

For this test, an analog (non-digital) voltmeter is needed. Do not remove the distributor connector from the distributor. Using small paper clips, insert them into the backside of the distributor wire harness connector to make contact with the terminals. Be sure that the connector is not damaged when inserting the paper clips. Attach voltmeter leads to these paper clips.

1. Connect the positive (+) voltmeter lead into the sensor output wire. This is at done the distributor wire harness connector.
2. Connect the negative (-) voltmeter lead into the ground wire.
3. Set the voltmeter to the 15 Volt DC scale.
4. Remove distributor cap from distributor (two screws). Rotate (crank) the engine until the distributor rotor is approximately in the 11 o'clock position. The movable pulse ring should now be within the sensor pickup.
5. Turn ignition key to ON position. Voltmeter should read approximately 5.0 volts.
6. If voltage is not present, check the voltmeter leads for a good connection.
7. If voltage is still not present, check for voltage at the supply wire.
8. If 5 volts is not present at supply wire, check for voltage at PCM 32-way connector (cavity A-17). Leave the PCM connector connected for this test.
9. If voltage is still not present, perform vehicle test using the DRB scan tool.
10. If voltage is present at cavity A-17, but not at the supply wire:

1. Check continuity between the supply wire. This is checked between the distributor connector and cavity A-17 at the PCM. If continuity is not present, repair the harness as necessary.
2. Check for continuity between the camshaft position sensor output wire and cavity A-18 at the PCM. If continuity is not present, repair the harness as necessary.
3. Check for continuity between the ground circuit wire at the distributor connector and ground. If continuity is not present, repair the harness as necessary.
11. While observing the voltmeter, crank the engine with ignition switch. The voltmeter needle should fluctuate between 0 and 5 volts while the engine is cranking. This verifies that the camshaft position sensor in the distributor is operating properly and a sync pulse signal is being generated. If sync pulse signal is not present, replacement of the camshaft position sensor is necessary.

Since you replaced the CKP, we can assume it is good for the time being. But I would inspect the flywheel for damage. A damaged flywheel will make a good CKP send a bad signal.