Yep, I think I will have to do that what you said. I use to have the third wire to starter years ago, but bought a starter years ago and was told I didn't need the "R" extra terminal. SO I taped it up and forgot about it in the tape wrap. Funny thing , the weather up here is colder then Calif and it has caused havoc with starting the truck in cold weather. Burned up about 4 starters and the recent alternator and truck just acted weird on starts where it had a hard time first thing in morning, but use during the day and it was fine. It would flood if I couldn't catch it just right on AM starts. I noticed on the coil wiring in the diagram there is a black wire suppose to go to coil, but can't locate it. Goes to the carb control box thingy and I bet its a ground wire. I think I have a crossed wire like you said or it's a ground wire not connected. I have been checking frame for stray voltage when at rest, but as you know, these wiring problems are very hard to capture if it only rears it's head during a load. Your right about these trucks wiring too, I have heard rumors about the wiring and mine has just began to cause headaches. That's one of the reasons I parked truck in garage and going through it with a fine comb. I should be getting my shortblock sent to me soon as well. Person to call me today or tonight I hope.
I have 275K+ on my shortblock, and 50k on everything else, surprised it hasn't blown the rings out making changes to head and not rings.
Anyway, I got to run some wires like you said, I may replace that starter I put in and buy one that has the R & S terminals to correct the inhibitor wire jumper on manual trany. Not sure I like the diode mod as much as the correctly wired starter.
I'll update this thread as I go through levels of frustration, lol