I might suspect bent or pushed back wire plug pins or failed splices in the wire harness from moving the wires all around for the motor install. Confirm the wire harnesses are properly located and properly secured to prevent insulation chafing on sharp metal edges or melting on hot parts.

Are all the engine sensors genuine Jeep parts ? Most auto parts stores sell cheap crappy Chinese made parts, some that even come with a "Lifetime Warranty". These parts are poorly manufactured and/or made from inferior materials. They are often out of specification, or even failed, right out of the box. The ones that are not faulty many times will have a short service life before they fail.

Did you have the crate motor put on a DRB-III Scan Tool and have the timing checked ? Installing a distributor only sets the basic timing, variances in parts tolerances may not result in proper timing, and the DRB-III Scan Tool ( or an oscilloscope ) can fine tune the timing.

Here is some P1391 info I have gathered.

P1391 - Intermittent Loss of CMP or CKP Signal. Loss of the Cam Position Sensor or Crank Position Sensor signal has occurred.

P1391 JEEP Possible Causes
- Faulty Crankshaft Position Sensor (CKP)
- Crankshaft Position Sensor (CKP) wire harness is open or shorted
- Crankshaft Position Sensor (CKP) wire circuit poor electrical connection
- Faulty Camshaft Position (CMP) Sensor
- Camshaft Position (CMP) Sensor wire harness is open or shorted
- Camshaft Position (CMP) Sensor wire circuit poor electrical connection.

P1391 - Possible symptoms:
(1) Random misfire/stumble/bucking/stalling, often over bumps or right hand turns or when going into reverse.
(2) Shorted out the Fuel pump/ECU power wire.
(3) A improperly indexed distributor/cam sensor may exhibit surging, light bucking or intermittent engine misfiring. This will most likely occur when the vehicle is at operating temperature and under a light load at approximately 2,000 rpm. The proper indexing procedure must be used as outlined in the service manual.

Often replacing the faulty sensor fixes the P1391 code, but not necessarily. Therefore it's important to check the following:
• Check that the sensor wiring isn't routed too close to sharp metal edges, or to hot exhaust parts.
• Visually inspect the wiring at the sensor for any burn marks, bare wires, or discoloration indicative of melting / chafing of insulation
• Visually inspect the cam sensor for damage. Make sure the magnet is firmly attached. The sensor can be tested.
• Visually inspect the reluctor wheel inside the distributor.
• If everything checks out okay, then test the Crankshaft Position Sensor.

If you buy any OBD-II engine sensors, make sure to buy genuine Jeep sensors.

Potential Fixes:
Fix #1:
Inspect your O2 wire harnesses for bent or pushed back wire plugs pins, damaged wires, chafed insulation, or failed wire splices. Use a volts/ohms multi-meter to check the resistance of the ground wire circuits from each sensor. Replace corroded ground wires/connectors and clean ground wire connection points.

Fix #2:
The timing may off. Re-index the distributor/cam sensor per the FSM instructions, or replace faulty distributor/cam sensor pickup module.
Read this article: Scan Tools, O-Scopes and Toothpicks here >> https://web.archive.org/web/20200820085756/http://jeep.blackonyx.net/pdfs/jcss.pdf
Read this thread >> https://www.jeepforum.com/forum/f19...ep-4-0l-p1391-potentially-p0351-p0352-p0353-crank-cam-sensor-issue-fix-3487474/

Testing the Throttle Position Sensor and Coolant Temperature Sensor is also a good idea.

 

Thanks for the possible problems and fixes. Some of it looks to be a bit over my head, but I can give some quick answers on certain things. First, I wanted to replace the CMP and CKP with genuine Mopar, unfortunately I was short on time, and of course no dealership within about 100 miles had either sensor in stock, or could have one within a day, so yes I used the cheap crap found in the chain stores. So I guess to eliminate the possibility I need to order Mopar parts, which I'll do regardless on Monday. As far as the timing goes, I thought on my model (1998 TJ ) that it was not adjustable. I don't have an FSM (someone gave me a link to one on here before but I could only get a small part of the manual to download) but in the Haynes manual that I have it says the the timing is adjusted by the computer...basically all you have to do is install the distributor(properly indexed) with the cylinder #1 @ TDC. I did remove the distributor, and re-check to make sure I had it set according to the Haynes book. After doing a quick read of the links you provided I think I can handle doing the sensor tests, after i get everything I need. There is plenty here to get me started
Thanks

 

Start with genuine Jeep sensors. Numerous 4x4 forum threads detail long and frustrating searches for a "problem" that ended up being cured simply with genuine Jeep parts.

At TDC timing "should" be correct, but if other inspections and remedies do not solve the symptoms, correct timing should be confirmed with a DRB-III Scan tool or an oscilloscope. The PCM can compensate for mis-timing, but not for a significant amount.

There are downloads of the Factory Service Manual that can be searched, or for about $15 you can buy one at www.pacificcoastmanuals.com. I find Chilton's and Haynes manuals work best when used for starting campfires or soaking up oil spills.

 

.

If find Chilton's and Haynes manuals work best when used for starting campfires or soaking up oil spills.[/QUOTE]

Agreed...but at least torque specs are usually correct.