No, I think you may be on the wrong track. You need to put the original computer back in, and then scan the PCM and PATS modules for codes with a Ford scantool like the NGS:
On your Explorer, the engine computer (PCM--Powertrain Control Module) communicates with the PATS (Passive Anti-Theft System) module every time you try to start the engine. If the THEFT light is involved, that means that PATS is the cause of the no-start. The PCM will only store one code to signify a PATS no-start: P1260. Any time the PATS is responsible for a no-start, the PATS module will also store codes. The codes will detail the reason that the PATS no-start occurred. So, if the technician only scans the PCM for codes, the PATS codes will not be found (some vehicles have PATS function integrated into the PCM, but yours is a two-box system where PATS and PCM are two separate modules).
The two-box setup also means that when a new PCM or PATS module is installed, they must be "married" to work together. The Ford scan tool must be used to perform the "Parameter Reset" which enables the new module to communicate with its counterpart. Once the parameter reset is performed, the two modules will only work together as a matched pair. The keys only need to be programmed if the PATS module is replaced, since the PATS module is the only one that "remembers" the key ID's.
The PATS on your Explorer is not equipped with a starter interrupt, so if PATS decides the engine is not allowed to start, the engine will crank over but never start. Read below about the behavior of the THEFT light. It sounds like the THEFT light is NOT indicating a PATS no-start with the original PCM, but with the new PCM, there is a mismatch between PCM and PATS since the parameter reset was not done. Therefore, THEFT is illuminated with the new PCM installed.
It sounds to me like you need a Ford trained tech to diagnose the vehicle. The PCM might be faulty, but at this point I don't see any evidence that it is definitely bad. The no-start could be caused by something other than the PCM. The PATS does not appear to be involved if THEFT is not illuminated when trying to start the engine (with the original PCM installed).
You can put the original PCM back in and it will still be "married" to the PATS module as long as the parameter reset was never done with the new PCM installed. If the original PCM does turn out to be faulty, then the new one can be installed, followed by a parameter reset performed with a Ford scantool like NGS. Then the new PCM can work with the PATS module.
Here is some basic PATS info from the shop manual:
The passive anti-theft system (PATS) contains the following components:
The passive anti-theft system (PATS) uses radio frequency identification technology to deter a driveaway theft. Passive means that it does not require any activity from the user. This system is known as SecuriLock® in North America, Safeguard® in the U.K., and PATS in continental Europe. This information can be found in customer literature such as the Owners Guide.
The PATS uses a specially-encoded ignition key. Each encoded ignition key contains a permanently installed electronic device called a transponder. Each transponder contains a unique electronic identification code out of over 72 million billion combinations.
Each encoded ignition key must be programmed into a vehicle's PATS module before it can be used to start the engine. There are special diagnostic repair procedures outlined in this manual that must be performed if the encoded ignition keys need to be replaced.
The encoded key is larger than a traditional ignition key. The key does not require batteries and should last the life of the vehicle.
The transceiver module communicates with the encoded ignition key. This module is located behind the steering column shroud, and contains an antenna connected to a small electronics module. During each vehicle start sequence, the transceiver module reads the encoded ignition key identification code and sends the data to the PATS module.
The control functions are contained in the PATS module. This module performs all of the PATS functions such as receiving the identification code from the encoded ignition key and controlling engine enable. The PATS module initiates the key interrogation sequence when the vehicle ignition switch is turned to RUN or START.
PATS uses the p owertrain control module (PCM) to enable or disable the engine. The PATS module communicates with the PCM over the SCP communication network in order to enable engine operation. The PATS module and the PCM use sophisticated messages in order to prevent a theft. The PATS and the PCM share security data when first installed together, making them a matched pair. After this security data sharing, these modules will not function in other vehicles. The PCM shared security ID is remembered even if the battery is disconnected. The PATS module also stores the vehicle's key identification code, even if the battery is disconnected. There are special diagnostic repair procedures outlined in this workshop manual that may be carried out if either the PATS module or the PCM needs replacement.
All the elements of PATS must be functional before the engine is allowed to start. If any of the components are not working correctly, the vehicle will not start.
PATS uses a visual theft indicator. This indicator will prove out for three seconds when the ignition switch is turned to RUN or START under normal operation. If there is a PATS problem, this indicator will either flash rapidly or glow steadily when the ignition switch is turned to RUN or START. PATS also "blips" the theft indicator every two seconds at ignition OFF to act as a visual theft deterrent.
PATS differs from the perimeter anti-theft system in that PATS enables and disables the engine from starting. If equipped, the perimeter anti-theft system protects the perimeter of the vehicle (doors, hood and trunk) and sounds an alarm.
The PATS is not compatible with aftermarket remote start systems, which allow the vehicle to be started from outside the vehicle. These systems may reduce the vehicle security level, and also may cause no-start issues. Remote start systems must be removed before investigation of PATS-related No Start issues.
The passive vehicle protection system will be activated and will disable the vehicle from starting if there is a:
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