That starter does look like a later model gear reduction starter, so you are good there.
Your harness is a bit rough, but I have repaired far worse. Anything can be fixed.
Start by removing all the PO added crap like that relay next to the head light switch. If it is a solid color wire, odds are it's not OEM, especially if it's red or blue...
Then use pics of a good harness to compare to what you have. If you are not needing Emissions, you can remove a lot of wires from that harness.
Now make a list of all the wire colors/gauges you need to repair and how many feet of each. Next do the same with connectors/terminals you need. E-mail that list to me fj40coolerman at gmail dot com. Note I also sell the non-adhesive harness tape to tape it back up after you have finished all the repairs/additions.
Once you get the OEM harness repaired, THEN go about adding any accessory wiring you may want like fog lights or power ports. There are two 1/4" male terminals on the back of the fuse panel. They are usually covered by heat shrink tubing. One always has +12V on it, the other has +12V when the key is on. You can use those for power taps for adding stuff. They are fused so you don't have to worry about adding separate fuses.
By embedding accessory wiring into the harness before taping, the added wires will look OEM to the next owner and make troubleshooting much easier.