1. Don't know what grommet you are speaking of. Old grommets are torn out and replaced with new.
2. Alternator: See comments below.
3. Relay: No horn relay on orig. So it was added. See comments below.
4. VR see comments below.
The difficulty here is previous owner wiring, alternator with external VR with old ammeter and 12V conversion and some fuses but maybe not enough and older restoration and a new harness that does not know all that.
Did you read my suggestion about marking and removing old harness as "one piece" of history to fall back on ?????? Following a harness that has the motor running "like a sewing machine" is a good way to proceed. There is NOTHING better than a harness to copy (if needed) that is modified, non original, hybrid, and works. We can explain the workings of a horn relay and ammeter wiring and external regulated and how an Echlin VR32 and alternator is wired and so on. But it will take three weeks of posts. We can do it but take my advice: carefully mark, write down, draw pictures, take pictures and carefully remove all of the harness in as few sections as possible. You said you took some dash harness out, did you keep it in tact and hooked up until documented? I know you may not wire some things the same but some you will. I don't know how to stress this further. Each wire in the removed harness can be "buzzed out" (continuity checked) to identify it's ends. Without tearing it apart.
Also still recommended taking all items mentioned earlier to the bench to refurbish and test. Then you are ready to install the harness. No offence, but your questions are hard to follow. Just unfasten harness leaving all components, except dash components, where they are. Take harness out as one complete ugly, branched, bundle if wire and tape. Lay it out flat somewhere safe for now.
Where did you get the diagram you posted? It looks like American AutoWire?? Is it the one that came with your LMC harness? Are there more sheets?
"Factory Fit" is a trademark name of AAW. Looks like AAW 30905. The LMC page 112 says in bold caps. "Harness does not come with wiring diagram." ? If your harness looks like the diagram, pre terminated contacts, terminals and connectors and is from AAW, you are in fat city.
The Voltage Regulator and Alternator is wired as follows. A big wire from battery terminal on back of alternator goes to battery positive post. One of the two alternator terminals (side-by-side) goes to the field terminal on Voltage Regulator. Ign terminal on VR goes to the ignition switch "on" terminal. (switched power). Alternator case must have good ground. Supposedly the other side-by-side alternator terminal gets grounded. Yours does not seem to have that and relies on case ground. Bottom line is: you will probably be using the new harnesses "generator" wires and it's old style "voltage regulator" wires as new wires for your alternator and external VR. Just repurposed and rerouted somewhat.
P.S. If it was me, I would change to internally regulated alternator now. This gets rid of the VR you have, Wiring is way simpler. Probably more reliable system.
Relay: We don't know if your relay is for the horn or for the lights or fan or is even being used? Does not seem like an old ooga had a relay, and headlights take two, and 12V does not need, but you have to tell us where each wire goes. Basically a relay gets a hot wire on one terminal, a switched wire on another and an output to a component on the third. This is an example of an area to document to either duplicate or understand and upgrade
Positive power can come from other places than direct wire from battery. They can bounce off starter, ammeter, terminal blocks, fuse panels, ignition switch and relays. Just convenient places to tap into power. So be aware of that when you are examining how your truck was wired/will be rewired. Previous owners doing "restoration", rewire, 12V conversion, Alternator conversions.... are liable to do many things.
If you see questions, answer them, like we are answering yours. If you are way past all this BS above and have it wired, let me know so I can delete.