You're overthinking this man! This ain't no nook plant but when that oem bulkhead connector goes up in smoke you will think it's a nookleeur disaster!
There are many shortcomings in most especially the Scout II electrical system, but really no more than any manufactured vehicle that was built by beancounters. The Scout II was a "clean but cheep" sheet of paper kinda design. When you compare the electrical system on those, with the systems that ihc manufactured for their real trucks which was the bread and butter of their business, it's hard to believe that they ever built any electrical shit like used on the Scout II!
So...once you start "helping" correct the design deficiencies on this old junk, it just doesn't end. That is why I shy away from "fixin" this old electrical shit and simply start from scratch with simplification and overampacity in component selection and wire runs.
I refuse to use relays for any accessory load on anything I do. The only relay I add is the starter relay and that is more of a convenience item than anything else. I hate relays...I spent years working in the auto manufacturing industry (all japanese stuff) as a field engineer and the asian shit is nothing but a mass of relays and light duty switching/wiring. That is a major reason why that "modern shit" is so expensive to service when it's "customer pay", with the pooter sensors, the relays, the multiple load centers, the sub-processors, and now multi-plexing going on, that stuff is where all the service work in a dealership lies today. And it never ends with multiple failures and multiple repair attempts because "technicians" today can't fix shit.
Typical service ticket at the dealership for that Ford ya just unloaded for a simple "battery won't stay charged" is over $1100 and you will return it at least three times before it's fixed right!
The reason for the multiple battery setups on this stuff I do is for trailer towing with trailers that have at least one and sometimes three large deep cycle batteries. Those batteries must be charged when dragging down the road!
The secondary use is for winching, where the auxiliary battery (or winch battery) is isolated from the entire vehicle system except when the engine is running to charge the battery. That totally prevents any additional load on the vehicle electrical system except for the alternator output which ramps up and down based upon battery(s) state of charge.
I'm no longer into this boombox/high end sound system schnizz (that is exactly why I have an 80% hearing loss!), but those amplifier systems the ricerocket/hot wheels/pocket car kidz run need huge battery capacity, with huge capacitors to handle peak current demands, that is why the multiple battery technology bizznizz has really taken on a life of it's own in the last several years.
My focus is to not end up with a dead engine crank battery when parked 50 miles out into the desert in a whiteout blizzard and 100 miles from the nearest 120vdc outlet ( I do carry a 1850w generator for a backup to the backup) and I've dry-camped for three days without cranking the engine. With an isolated system, the crank battery cannot be discharged except by parasitic load.
I rarely install any alternator that has a greater potential output that the oem 61>63 amp unit. I see no need for that unless I was running many 12vdc accessories such as in a "portable" shop trailer. I have no need for the multiple high current draw offroad lights in my world and most of that stuff ya see rolling down the road is all show and no go (except in texas where we used them lights for jacklightin' rabbits and coyotes at 2ayem).
If one were building an "expedition" vehicle, then that is special purpose-built stuff and the sky is the limit:
ecoroamer | traveling the world, one dirt road at a time.
The auxiliary power distribution stuff is simply for convenience and to eliminate running wires all over the place inna haphazard fashion. By doing this no additional load is placed on the oem vehicle electrical system/wire runs/switches, the additional loads do not pull through the oem ammeter circuit at all. Therefore, there is no additional load on the shitball oem bulkhead connectors or the alternator/battery charging wire runs.
The "factory" protection as implemented on the Scout II varies tremendously from the beginning to the end of production! You can see the "fusible link" issue raise it's head around here on a weekly basis. But in the late 60's through the 80's, the fusible link was current technology for system protection. However, there was no master protection for the entire system. And worse, after 35 years of bein' po'd, this stuff has every kinda workaround known to man regarding "fixing" electrical issues. Many of the systems I see have had the fusible link(s) totally bypassed or eliminated simply because they fried. So instead of repairing the root cause, let's just eliminate the protection??? Then we can whine when the whole pos goes down in flames in the parking lot!
Your sii, right now, should have a 14 gauge fusible link for system protection of the feed to the fuse panel and the interior electrical loads. That is roughly equivalent to a 50amp fuse, but a fusible link will handle about a 20% overload intermittently before going into hard failure.
Modern vehicles also have various forms of fusible links (mostly the plug-in type). So they have protection on top of protection. Wanna deal witha bitch? Screw around with the multiple load centers, and "fuse panels" incorporated on Ford superduty trucks from the mid-90's on. I deal with those constantly since all my buddies drive that shit, they loose electrics/loads constantly on those rigs for no reason at all. And the Ford dealer will kill you in diagnostic charges and still never actually "fix" anything. The relay array alone is mindboggling. I consider the Ford superduty diesel to be the ultimate throwaway vehicle. Throwaway front axle/steering/brake components, throwaway driveshafts, throwaway fuel systems, it never ends.
The cooper/bussman-type fuse panels are hanging on the wall even at autozoo locally. And every other auto parts carries 'em on the wall also usually where all the fuses and light bulbs are:
cooper bussmann ® - blade fuses and accessories
For the much higher quality stuff I use the qwikwire stuff such as this right here from ihon:
kwik wire ~ add on fuse blocks
Or the marine-type product such as available from blue sea:
fuse blocks & fuses - blue sea systems
None of this additional load center stuff (or loads) really impacts the alternator, a delcotron 10si is a real work horse with a fairly decent duty cycle if it'sa reman of high quality parts, most especially not a chinee internal voltage regulator. I use only reman alternators done by a local quality rebuilder. I do own two autozoo "lifetime warranty" units that are kept in the truck box in each rig in case of emergency when on the road. I do that because they are swappable nationwide wherever we May be. These are set up with machined pulleys already and have been "clocked" appropriately for each vehicle also.