There should also be a connector for the clutch switch in the auto harness, taped up above the pedals. It'll have a shorting jumper plugged into it for use with the auto; just unplug the jumper and then plug the connector into the clutch switch on the newly added clutch pedal.
I've done an auto to manual conversion on a '90 Bronco II using a '90 Ranger for the donor (both 2.9L and 2WD). On mine there were no differences on the ECM connector pin-outs, besides the auto shift solenoid output (which was simply not present on the manual ECM). So on mine the manual ECM simply plugged in to replace the auto ECM. BUT, yours being a little later, and 4.0L, I can't say if yours will be that easy. I used the wiring diagrams in the Ford EVTM to compare and confirm that mine were compatible without needing to re-pin any wires at the ECM connector.
The only other wiring that comes to mind, was the short harness underneath going to the transmission. On mine all I had to do change out the original auto short harness for the donor's manual short harness.
Hope that helps; good luck!