The PCM code on the door is the calibration code. It defines what control strategy and what calibration file have been burned into the PCM memory. There is a 4 digit code shown on the boxes that PCMs are in when shipped to the assembly plants. This does match the code on the PCM harness connector. If you buy a service PCM, the dealer has to burn the code into the module, and that is done based on the vehicle VIN # and what the Ford Service computer aligns for calibration updates to that vehicle package. It also prints new lables. Often the dealer does not update the door code, but it should be on the cam cover or in engine compartment as an over lay decal.
My 1998 4x4 explorer has calibration "CGU" on the door post and BAE1 on the PCM harness connector. I do not think these two codes provide the same information. BAE1 is the PCM module family configuration, what features and what pin-outs. "CGU" is the calibration my car was made with at assembly plant. Maybe some knows more, if you find out, please advise.
If you have the engine harness, all the injectors, TPS, ECT, sensors, to the large square connector mounted above the driver's side cam cover, and you have the mate to that large connector that includes the sensor and control plugs for the trans as well as the PCM connector, you have all the wiring needed to control the engine and trans. Make sure you have the MAFS, mass air flow sensor, and harness. The ACT, air charge sensor, is mounted in the plastic tube that connects the MAFS to the throttle body. You need this too.
FInd your self an Explorer or ranger with the 4.0L SOHC/5R55 and see where the vheicle interfaces to those harnesses you have. Vehicle power, ground, crank and run signals, the fuel pump relay, etc all have to connect up to your harnesses. Account for every connector on your harnesses, and make sure you know how to reproduce that connection on your old truck.
If you can't figure one out, ask, we have 4 such vehicles in our family fleet. Let's keep talking.