Its not technically part of the engine wiring harness, so you may not have pulled it out of the 4.0l donor
The 1989 manual trans cab harness should have the clutch switch wiring in place
There should be 2 Pink wires going into the clutch switch, one comes from the ignition switch and the other goes to the firewall where it changes to a Red/light blue stripe wire in the engine bay
The red/light blue wire runs to the starter relay(solenoid) on the inner fender, it might have been taped inside the 2.9l wiring harness, so cut or removed when that harness was pulled out
The 1991 automatic would have had an NSS switch on the drivers side of the transmission, its wiring harness would have the same 2 Pink wires, one changing to red/light blue in the engine bay
It would also have the Backup Light wiring, purple/orange and black/pink
The computer wiring is not involved with starter motor activation