No, it wasn't clear.
You had a problem.
You replaced the CPK.
You had a slightly different problem.
You put back the original bad CPK.
Still have a problem.
Not sure that proves anything.
Did you install the OEM CPK yet?

Update to this nightmare. I installed the dealer supplied CKP/CPS, found the $15 CPS wires had melted. Replaced coil, dist cap, rotor, plugs. Jeep ran for about a day then would not run again. Had a garage install a Bosch fuel pump assembly. Drove the Jeep home (3 miles) died three times before I parked it then would not start the next day. Installed rebuilt PCM. Jeep ran great for the rest of the day (20 miles stop and start). This morning died at least a dozen times in a few hundred yards.

What I have found that remains consistent with this problem is that the fuel gauge will read below the actual level. Example; there is currently 1/3 tank but gauge will read E or below. The fuel light will not always be on. When the Jeep runs fine the gauge reads accurate. I am thinking that since the fuel gauge seems to be involved in this that I might be looking at an electrical issue. I haven't yet ruled out the new Bosch O2 sensors since I read on a post that Jeeps don't like Bosch O2.

Any help here is greatly appreciated.

One thing I haven't seen in here yet. Have you done a TOTAL refreshing of the grounds? Cruiser54 has a good writeup for the Renixes (Renices?) that should get you started. All grounds should be undone, scrubbed clean and shiny with something abrasive, hit with electrical contact cleaner, and reassembled with a conductive grease like Gardner Bender OX-GARD or Sanchem NO-OX-ID. This stuff is NOT the same as dielectric grease. They are used in the telecom, electrical, and radio industries for preventing corrosion (such as aluminum-to-copper) and improving connections. I've used the Sanchem goo to restore function to a rusted headlight socket. Dielectric grease, on the otherhand, is an insulator. Also do similar for all connectors, relays, and fuses, though minus the sanding bit where appropriate. Even if this isn't the problem now it's still great maintenance.

Have you done the ignition system and checked the ASD relay yet?

Hi Salad - I have not hit every ground yet. I swapped the ASD and Fuel Pump relays with no improvement and even swapped in a new relay and moved that between the two but no improvement.

What are you referring to when you say "have you done the ignition system"? I have changed the coil (two grounding points on the coil mount bracket were tightened but not properly cleaned), cap and rotor, and plugs. I did not change out the wires. My reasoning here is that bad wires would likely cause rough idle or other similar problems in varying conditions, maybe even cause the engine to randomly shut off, but how would it affect the fuel gauge?

Was just a thought - coincidences do happen lol. Yeah what I was really thinking of was the coil, possibly the coil->distributor wire too. Grounds are definitely a biggie and will cause all variety of issues.

I know on the Renix models the CMP (CaMshaft Position sensor) isn't required to run but not sure on the OBD2 models... will see what my FSM says. You might get a few hits on searches here in the mean time for CMP related issues. (If you weren't aware you can add "site:cherokeeforum.com" into Google and it will look here - beats the snot out of the in-site search and keeps out the shmucks from Yahoo Answers and eHow)

Okay so it's not entirely clear from my 1999 FSM what the failure modes for the CMP are or how it should be tested. I think others have replaced it in the past to solve a no-start problem.

You're getting fuel sprayed out, right?

Salad - I am going to follow your lead and look at the Camshaft sensor, or as AutoZone calls it, the Pick-up Coil (#CR149). This makes sense to me that if bad or shorted could bounce around and make intermittent contact. If this happens, an intermittent ground or short could affect the fuel gauge. Maybe total BS but it sounds good! Of course I still have the grounds to work on too.

What Scanner do you have? It must be an OBD II scanner inorder for you to even plug in to the Data Link Connector. Does your scanner "communicate" with the vehicle at all? With the problems you are seeing, there has to be diagnostic trouble codes stored in your PCM, either set or pending. It is important to resolve your scanner problem inorder to see what codes may be stored. If your scanner is an OBD II, it should be able to communicate with any OBD II vehicle. If it simply cannot turn on when plugged into the DLC, there may be a bad ground for the DLC (two wires connected to the oil dipstick tube attach bracket). Power to the DLC comes from fuse #17 in the PDC, but it also powers the dimmer function of the headlamp switch. If it won't "communicate" with the vehicle there may be bad contacts in the DLC for the Serial Communication Interface (SCI), which are required for the scanner to receive data from the PCM. Examine each pin socket in the DLC for corrosion, enlarged pin sockets, or pin sockets being push back in the connector. Check/clen the DLC grounds on the engine.

You may be experiencing a CCD Data Bus problem, either from a bad module, PCM, or defective wiring. Your CEL comming on intermittantly shows that the PCM is trying to communicate with your instrument cluster, but can't hold the CEL for some reason.

Try this Instrument Cluster Actuator Test. It will show if the CCD Data Bus is communicating with the instrument cluster. The test checks the PCM, the CCD Data Bus wiring, and the instrument cluster. Note the "Check Engine" light function and your fuel quantity indication, amongst other lights and instrument functions. Go through it several times f required to catch all functions and to see if it's intermittant. You may want to use a helper to wiggle the wire harnesses around the PCM and along the firewall to see if any changes take place during the test.

Get back with any/all results from this test and answers to the above questions please. If your scanner is an OBD II, it should be able to communicate with any OBD II vehicle

Instrument Cluster Actuator Test

(1) Begin the test with the ignition switch in the Off position.

(2) Depress the trip odometer reset button.

(3) While holding the trip odometer reset button depressed, turn the ignition switch to the On position, but do not start the engine.

(4) Release the trip odometer reset button.

(5) The gauges should cycle through their ranges, stopping at intermediate readings, going up and going down, at two second intervals. The indicator lamps should cycle on and off.

(6) The instrument cluster will automatically exit the self-diagnostic mode and return to normal operation at the completion of the test, if the ignition switch is turned to the Off position during the test, or if a vehicle speed message indicating that the vehicle is moving is received from the PCM on the CCD data bus during the test.

Thank you for your help CCKen. I have my fingers crossed that the problem has been solved after I changed the Camshaft Sensor (or as AutoZone calls it the Pickup Coil). I was able to drive the Jeep into work today (7 miles) but that doesn't necessarily mean it is fixed. I want at least a week of driving without issue before I call this fixed.

My Scanner is a cheap Chinese scanner I am sure, but it is OBDII as I have communicated quite easily with several 20xx model year vehicles including my 2005 Altima. My issue with the scanner and the Jeep is that the scanner is not reading live data from the Jeep but it will read live data from other vehicles. This is true with the "rebuilt" PCM as well as the original PCM.

Since I finally have the vehicle here at work I am going out right now to do your Instrument Cluster test. Just to clarify though, I have not experienced an intermittent CEL. My CEL is only on in conjunction with the vehicle stall/die/cut-out issue.

UPDATE:
It is approximately 1 week since I changed the camshaft sensor and the Jeep has run every day with none of the previous issues. As soon as I find some wood to knock on, I am calling this fixed!

I believe that I did have more than one issue going on from the beginning and not all of the parts that I threw at this problem were unnecessary.

So to re-cap the list of parts changed -
Crankshaft Position Sensor
Distributor Cap
Rotor
Spark Plugs
Throttle Position Sensor
Ignition Coil
Fuel Pump (Bosch)
Power train Control Module
Camshaft Position Sensor (aka Pickup Coil)
Mazda 626 (I got sick and tired of bumming a ride everywhere!)

I still have to freshen up my grounds and I want to replace my battery cables with thicker welding cable and change the Valve Cover Gaskets to keep oil from leaking on the various sensors. But for now the Jeep is running and able to transport me to and from work. This is a very important thing given the amount of $$$ I have thrown at this problem.

Think of it as an investment in the future. Much of those parts often fail eventually anyways.

Great news, thanks for the update!