Alternator upgrade ??s

Dale Davies said
Well, just changing to a higher output alternator is not the end of the job. Are you using the stock ammeter? The a.meter shunt needs to be capable of the current you will.put through it. Take the original 60 amp off and install a 100 amp and if you draw the 100 amps, the shunt could get hot and cause a failure or fire.
I worked on an ambulance once and installed a 100A alternator to power extra equipement they had installed. Melted the ammeter. The wiring to and from the ammeter where charging current will flow also needs to be up to the job.
In normal operation the alternator should only output the sum of all the draw of the end devices. Temporary items such as power windows or locks are surge power and not generally a problem. Lights, AC or a high power sound system create that long time draw that builds heat. That was the problem for the ambulance, a new baby incubator and 3 hour transfer times from the small town.
Sometimes best to connect the two ammeter wires, remove the ammeter and install a volt meter.

The probalem with all of this stuff is trying to run all that electric (whether its the ambulance extras or the EFI extras) on a wiring strategy designed around totally different requirements. All the standard system needed to do was (a) start the engine (b) allow the alternator to run a few items and recharge the battery. The highest loads were battery and that was just for very few minutes, and then lights and 'accessories' like wipers and heater blower.

That's pretty much out the window with the OP's car. It needs a bunch of electric power at all times just to run the engine. During start the battery draw down will be higher than factory, meaning the recharge will be higher given power at the same voltage.

I'd suggest redesigning the system. You don't have to toss all the original - some subcircuits may be fine. Focus first on the main feed or feeds. Whether you want to use the battery as a filter depends on your electronics. Not a concern on the origina l system but may be with your stuff.

Discussion here about a Chrysler RV with two batteries but not quite the same issues as running loads are very basic other than the RV battery recharge needs.
https://www.forabodiesonly.com/mopar/threads/ammeter-to-voltmeter-who-does-it.119480/page-7
if battery is not needed in between the alternator and the electronics, then a strategy like this can be used (with or without an ammeter). if using an ammeter consider a shunted unit or one made for the recharge/discharge loads expected.

or have a second fuse/relay box in the engine compartment

The alternator output wire in the diagram above still needs a maxi fuse or fusible link between it and the battery in case the alternator shorts.
https://www.forabodiesonly.com/mopar/threads/fusible-link-or-not.458737/post-1972905524