Wiring Modifications
This section will be how to modify and install your Scout 2 wiring harness to the late model(78-80) wiring with the GM style fuse box. You will need several rolls of good quality electrical tape, buy the good stuff, it will make a difference. And you will also need several sizes of high temp split wiring loom 1/4 up to 3/4, again buy good stuff.
I had an inline fuel filter (aftermarket) split on cold start up one spring and it sprayed fuel on the headers, instance fire! This was on a cold engine running less than 30 seconds! That short fire took out the fuel pump, alt, and belts and blistered the under hood paint, but the wiring was saved by the high quality loom that I used. I did have to replace some loom as it was slightly melted, but the wiring and tape was untouched.
On my 73 Scout I upgraded the factory fuse box to a late model GM blade style box because it was more modern, and I needed more fuse openings for my EFI project because I did not want to have to add on a second fuse box for that. Also the factory style (IH) has one fuse for as many as 4 circuits, my setup uses one fuse for each circuit. This conversion is not hard, but it takes time to do right.
I started first by getting a donor harness that was not modified by anyone or was in bad shape from overheating. Get the inside dash harness, the engine/headlight harness, and the tail light harness. If you have cruise control, you can either get that with your new harness or you can re-use your old one as they are the same.
The easiest way to do this is by using a 4x8 sheet of plywood as a template/guide. Lay out the harness then use finish nails to hold the harness in place as you redo it. Start by removing all the old loom and then inspecting every wire and connection. Repair and broke or chafed wiring the fix any connectors you find. I also used a Dermel tool with a wire brush to clean all the grounds and any dirty connectors. Then cut out the old tape and re-tape everything about every 6 inches of so. Clean the wiring as you go but DO NOT use anything stronger than water or you will wipe all the factory wiring markings off, not good! Repeat this on all three harnesses and the cruise control harness as well. The factory taped the tail light harness from the engine bay all the way back to the rear of the truck but I loomed mine because it looks better and the loom will protect it from sharp objects.
There are several modifications you can do to the wiring, like upgrading the charging circuit, moving the main power feeds from the starter to the center of the firewall, adding a section to power any upgrades like aftermarket lighting, adding relays to remove heavy loads from the ign switch and better tail light sockets, I will also cover these mod's on another section.
Once you have you harnesses re-built, then you need to strip your truck of all it's old harnesses and modify the firewall for the later model style harness. Below are a few pictures of the old style firewall wiring holes.

These are before pictures, with wiring and without.
First step after removing the truck's old wiring is to modify the drivers side firewall for the new fuse box. In the picture above, left you will notice the small square hole were the early style harness went and a small hole above it. That small one is for the cruise control wiring. Some scouts have them there and some have them more to the right, It might depend on who cut that hole at the dealer or the factory. You will need to make sure you leave that hole functional if it's right about the new fuse box location or plug it and move it some were else. I left this one were it was, it's tight but a little care and it's not a problem. Below it a picture of the new hole I cut for the new wiring. the second picture is the view from the engine side with the dash harness in place, just enough room for the cruise control wiring.

Next you will need to modify the passenger side firewall for the new harness. The first picture is before, and the second is after cutting out the section in between the two original squares. You will have to cut the opening just a little bigger than the plug it's self.

Then you will need to make a plate to mount the late style plug that resembles the original opening. The plug goes in and twists to lock in place. Left is the plate installed. I used stainless steel screws and a thin foam type gasket behind it. Right picture is with the plug installed.

Next I mounted a "standoff" for the main power cables to meet up, you can see some of it in the lower right bottom of the second picture above. One cable comes from the battery, one from the starter, and one from the alternator. Also, the main power feed to the amp gauge has been moved from the starter to the "standoff" I always bypass the amp gauge on my Scouts because I don't run stock alternators because I'm always adding more lights, ect. The fourth one goes to a second "standoff" for extras that I add on later like off road lights, stereo amp, ect. This is the post I power all my relays for any add-ons like lights. You always want to run those type of loads through a relay and not a switch.

Next pictures are of the starter wiring and ground strap/alt. I always run a ground strap from the block to the firewall, block to the frame, and battery to the core support. If you don't run enough good grounds, the electrical system will use the next best ground path, the shifter cable. Most of the time if will weld it's self solid or just break when you try to shift it.

The wires running to the alt are ran along the inner fender to keep them away from the exhaust. The starter wires are also ran away from the exhaust instead of over the top of the starter and back like factory. The only wires now on the starter are the battery cable, the crank wire and the wire sending out 12 volts to the coil during starting. I am running headers with no heat shield on my 73 Scout and have not had a problem in 10 years.
Below is a picture of the installed late model fuse box. On the left is the relay setup that I made to remove most of the load from the ign switch. One relay handles the load for the A/C blower motor, one handles the load on the ACC side of the fuse box and the third handles the ign system. The third one is not really needed, but I set this up for use with an alarm system so that when the alarm is set off it will ground the ign circuit that way it can't be hot wired. I also installed a hidden switch that when turned on it will also ground the ign circuit. I used a reset able breaker fuse so if the relay is grounded by the alarm or by forgetting to turn off the switch it won't blow the fuse requiring replacement because I hid the fuse way under the dash were you can't get to it without lot's of work even if you know were it's at.

Next I made a relay setup for the headlights, one relay for low beam and one for high beam for each headlight. This removes the load from the headlight switch and will provide the headlights with full battery voltage at the light. You would not believe how much brighter the lights will be after this mod. With the stock set up you might get any were from 9 to 11 volts at the lights, with the relay setup you will have a full 14.5 volts. This might not seem much, but it will make your light twice as bright and you headlight switch will last for almost forever. the picture on the right is were I mounted the fuses for the relay power feeds. You want the source as close to the battery as possible to avoid voltage drop. I used a 20 amp fuse for each relay feed. The feeds to the relays go right to the positive battery post. You can either make this relay set up yourself or one of the vendors sell something like it. With my set up I cut the factory wiring and ran it right to the relays, the ones you can buy are setup to plug into the factory wiring so you can put it back to stock if you want.

Next section is wiring diagrams for relay centers and the headlight relays.