On a 98 Eddie Bauer 5.0 Explorer, Does the GEM have anything to do with the Vehicle Speed Sensor signal getting to the PCM?
Looking at the wire schematics I see the same wire color (GY/BK) connects 9 components.
Message Center
GEM
Instrument Cluster
PCM Pin #58 (Vehicle Speed Sensor Input)
Speed Control
Outside Air Temp Module
Air Suspension Control Module
Radio
4WABS
The PCM pinout shows Pin #58 (GY/BK wire) is for the VSS Input (I am assuming they mean Input Shaft VSS) and Pin #84 (DB/Y wire) is for the Output Shaft Speed Sensor. (These would be for the original automatic transmission.)
I swapped this engine into my 54 F-100 with a T-5 manual transmission from a 91 Mustang. The T-5 only has a VSS connection on the output shaft.
I have a VSS Sensor to install on the transmission and a cable to adapt to my mechanical speedometer.
The big question here is, Will the PCM be happy with the signal only from the output shaft of the transmission to pin #84 and does the VSS also need to be connected to the GEM?
I don't see any of the other components in the list that would make a difference in the operation of the engine.
Can the VSS simply be connected to the PCM at pin #84 since it comes from the transmission output shaft without having the GEM or anything else involved?
OR......Will the PCM not even be able to use the signal without something connected to pin #58 for the VSS input?

Comments and advice please and thanks for your interest.
Bob

UPDATE: 12/14/2020
Another thought I had was that since the automatic transmission has been changed to a T-5 manual transmission and deleted from the PCM, would the PCM not need the signal to regulate any transmission shifting requirements but only for smoother engine operation?
This morning I carefully inspected the PCM connector to see and make sure the correct wires as shown in the wire schematics were at Pin # 58 GY/BK and Pin # 84 DB/Y. Come to find out the wire at Pin #58 is in place but there is no wire and never has been at pin #84.
So, the only place on the PCM to connect the VSS is Pin #58 which according to the pinout is for the VSS Input. Why there is a blank pin # 84, I don't know. Any ideas will be much appreciated.

The main reason I am asking these questions and relating what has been done is because the engine starts and idles and runs very nicely but will stall when coming to a stop. (however not every time)
I removed the EGR valve and sensor along with a few associated vacuum lines and had it deleted from the PCM. I did a smoke check on the vacuum system and all is secure with no leaks. I the checked the vacuum which shows a good 20 to 21 inch/ag at idle so I am pretty sure the vacuum system is not the problem. The Intake Air Bypass Valve is new and give a normal idle of around 650 RPM. At this point all I have left that is not connected is the VSS. Could this be the cause of the intermittent stalling problem?