The EEC from the 88' currently does not have a pin in #3 (VSSDIF +) or #6 (VSSDIF -), can I wire the speed sensor wires from C350 (dark green/white, orange/yellow) directly into the respective 60 pin slots? I'm guessing the last setup did not have the VSS sensor because the connector is not in the harness, nor anything wired to the ECM.
Yes, you can wire the VSS directly into pin 3 and 6. The 86-88 cars ONLY use the VSS for the cruise control so they lack the direct wires to the ECU. In 1989 (or Ca '88 Mass air cars) they were added with mass air ECUS. The above graphic should really say 89-93, although wire colors did change a bit from what is shown.
For the neutral gear switch, what is the purpose of that switch if the clutch switch is being used? I am looking at the following schematic.
The schematic is incorrect unfortunately. Hard to describe, but they are related to pin 30, but separate and do different things.
The clutch switch is what prevents you from starting the car in gear. There is no transmission neutral safety switch as it's only used for the automatic cars, and just jumped out on the 5-spd cars. Clutch switch is the only safety on the starter circuit.
The NGS does tell the ecu if the trans is in gear, but only for the sake of code-reading, and it does affect idle strategy somewhat. Not having the NGS hooked up can
sometimes cause a hanging idle on a EFI car. The NGS on the T-5 is wired in parallel to the clutch switch on a separate leg of the switch.
Here is the clutch switch (down below). Notice there are two pairs of pins. One is the starter interrupt circuit. The other is the pair of wires that is wires in parallel with the NGS on the T-5. So essentially, if EITHER the clutch is in or the trans is in nuetral, a signal is sent to the ECU on pin 30.
This is probably the most confusing aspect of how Ford wired these cars, because it's different between auto and 5-spd cars, and as a result can fry a ECU if you use an Auto ECU with 5-spd wiring, and the other way around.