OK here we go:
- mysterious connector in the back, drivers side = no effin clue, don't look factory to me. What are the wire colors on it, if you can see them?
- larger back bumper hole, left side = factory location for license plate light. There should be two of them, on each side. It's fairly common for people to take one out and stick a small (5-pin or 6-pin) trailer connector in its place, saves them the effort of cutting a new hole in bumper. The two screw holes are for the connector, from the factory they do not exist.
- smaller hole, right side = possibly a different trailer connector, this one looks sized for a 4-pin one.
- thick wire, run from the front to the back = anyone's guess at this point. Could have been used to power a winch that goes in trailer hitch receiver. Or really anything else that draws a lot of power. Cap it off properly, and leave it in place for future use, I'm sure you'll find one.
- upside down toggle switch = another NFC item. Where do its wires go, can you trace them?
- glow plug wire to relay, stated amperage size = that's a 6 gauge wire. My suggestions would be to pull it from the glowplugs relay and put it on the starter relay, and at the same time pull the black cable from the starter relay and put it glowplugs relay. Basically swap their places. Reasoning: starter relay and entire truck will be just fine with 6 gauge (actually even that's a bit overkill), while glowplugs relay can definitely put the larger 4 gauge cable to good use (plugs draw well over 100 amps). You already have the cables, might as well use them to their max potential.
- different view of wire size = almost looks like someone use a stranded household 14-3 cable, since it has green and white and black wires all run thru a common sleeve. Won't be the first time I've seen it done, and it actually works pretty good for keeping wiring organized. As to what purpose it has in your truck, that idk, looks like another trace the wires project for you...
And yeah, seems I was right on the starter cable - basterds cheapened out. Supposedly early 6.9 trucks had 2/0 between the batteries and 3/0 to the starter, then Ford figured they can slide with 2/0 all around and the aftermarket followed suit. No big deal, fresh and clean cable trumps old corroded one any day even if it's slightly smaller than it. Run it an enjoy it.
As for pics, if you can take one that is sorta zoomed out view of everything on the fender, would help visually tracing wires. Set your camera on the engine air cleaner, that should give a decent picture of the whole spaghetti mess.