Will not start after replacing both speed sensors on the 4WD Transfer Case

Thanks for the reply. I plan on checking the crank shaft positioner signal at pins 21 and 22 on the PCM with a scope tonight or tomorrow morning. Could the Passive Anti-Theft System (PATS) be stopping the car from starting? I do not drive this car and I did notice the theft light in the dash pulses when I turn the key on.
In addition, I found a used computer at a salvage yard that matches all the information on my PCM. Can I drop it in my vehicle or is there some kind of information shared with the PATS system which requires a Ford Garage to re-program? I heard that on a Toyota computer you can short out some pins for 20 minutes and it bypasses the theft devise & will let it start your car forever without reprogramming. Does a Ford 2000 Explorer PCM have any tricks required when replacing it?

Thanks

Thanks again for the reply. I have learned that the theft light pulsing slowly is normal. When it flashes fast is when it locks you out. Also, the light only pulses slowly until I turn the key on then it goes out. I put a scope across pins 20 and 21 at the PCM and while cranking I saw a sinusoidal wave with about 2 volts peak-peak. Is this normal? With the main transfer case plug still unplugged (no shift motor or speed sensors), I replaced the GEM module. All normal functions worked (radio, windows, locks, wipers, etc.) But still no spark. I then installed the spare PCM that I bought today still no spark. I rechecked all relevant Transfer Case and PCM fuses and all were good. Checked for faults using my Actron CP9580 scanner and none were reported. I assume the spare PCM did not work since the Key is programmed for the original PCM. Can a Ford Garage check my two PCM's and program my key to the good PCM? Not sure what to do next. I may install the new crank shaft position sensor just to eliminate it (was only $22.00 at AutoZone). Any suggestions would be greatly appreciated.

Thanks

Thanks again. I replaced the cranks shaft position sensor last night and disconnected the battery to reset both PCM and GEM overnight. Plugged the main plug back in at the transfer case before reconnecting the battery. I then turned the key on (not to the start position), pressed the brake pedal, and cycled the 4WD from Auto to High to Low and back to Auto so the GEM would find its position. The car started & the previous 2V peak to peak sinusoidal crank shaft position signal went off the chart. I thought I was good, so I turned it off, closed the hood and cleaned up. I then went to remove the car from my garage, and it would not start. I opened the hood, checked all fuses - okay, repeated the 4WD position switch cycle and it started. I drove it out the door and noticed the front wheels binding while turning in my driveway. I then flipped the toggle switch, I inserted previously to disengage the transfer case clutch, and the car shut off and would not re-start. I then pulled the fuel pump relay to recheck for spark and feedback from the new crank shaft position sensor. No spark and back to the previous 2V peak to peak sinusoidal crank shaft position signal. Rang out the crank shaft position sensor plug back to PCM pins 20 and 21 which were good. I then disconnected the battery to clear any faults in the GEM and PCM. After a half hour my cousin showed up with a good scan tool to check faults on the GEM. The car started again, and he cleared about twelve different faults which did not come back. However, the car shut off after about 1 minute. It then started right back up. It did this 3 or 4 times while he monitored for faults. Then it stopped and would not start again. After running a few test sequences using his scan tool it started again and continued to run without ever shutting off again. He had me unplug the Cam Position Sensor to show me the car would continue to run since it only needs this signal to start. Thus, the Cam Position Sensor was not my problem causing the car to just shut off on its own and leave no faults. He suspects the problem could still be with the new crank shaft position sensor or a relay dropping out. We swapped Relay 4 (PCM power relay) with Relay 9 (blower motor relay) while troubleshooting but it still did not start at that time. Also, while the car was running, we banged on the fuse box under the hood and wiggled the PCM connector trying to get the car to shut off. The car would not shut off. I just got back from running the car for at least a half hour to enable the PCM adaptive learning and it is running fine. I left my brown wire clutch disable switch in the off position eliminating the automatic 4WD. My cousin owns a transmission shop and said I will still have 4WD and the clutch is only used in auto. At this point, I plan on running the car as is with the automatic 4WD disabled. Finally, he said if the problem comes back that I should perhaps buy a better crank shaft position sensor. The new one is a Duralast SU2032. The original sensor was covered in oil and dirt and rings out at 380 ohms while the new one is 468 ohms. If it acts up again, I may clean up the original and re-install it. Any thoughts on what was causing my issue? Any suggestions on what to do next if the problem returns? Any advice would be greatly appreciated. I will let you know if the problem returns.

Thanks again!

All necessary grounds and the power feed on the PCM plug were verified. I believe it may have been a coincidence that it shut off when I engaged the transfer case clutch the one time since it started and then just stopped several times randomly prior to the problem just going away. When it did finally stay running my installed disconnect switch was on putting the clutch in the system. I shut the switch off later just as a precaution so my wife could use the car for work. The new sensors are still in the circuit, so I guess they were not bad causing my problem. I’m not sure what happened, it’s almost as if the longer it ran the adaptive learning in the PCM and GEM modules possibly cleared the problem. Any suggestions on what to do next if the problem returns?

Thanks