Ron,
I have donned my Nomex in preparation for my response and opinions. I am sure it will probably open lots of opposing or alternate dialog.
Anyway, in my opinion and experience you should address the areas where you have observed the excess heat. You have the proper equipment and skills to overcome the factory deficient splices and crimps. Do not use the cheap PVC insulated connectors. Buy the good ones, preferably with the nylon & heat shrink. Clean up (cut out) any wiring that has been exposed to the excess heat. The addition of the new fuse block will eliminate most of the heat affected wiring. The headlights and heater fan circuits can be addressed individually. The ammeter should be checked for a good, tight connection on both terminals. Don't get too aggressive here as the plastic is delicate...just nice and snug. If it has the slip on connector just crimp the connector enough for a good, tight contact. Sounds like yours is OK.
The main power line at the bulkhead connector is a challenge as the plastic block as well as the spade connectors are usually melted beyond repair. I have drilled out enough to run a proper heavy gauge wire through the cavity with a properly sized butt connector for union. On some I have silver soldered, or used regular solder then used overlapping layers of heat shrink on splices as well as crimping on others. It is your choice, but I have found using the right tools and connectors that a good crimp and high quality connectors with built in seal (heat shrink) makes the job quicker and lasts just as long, without the potential detrimental use of high heat and corrosive flux effects in the long term.
I am very anal about having functional equipment in my vehicles; if it came with the vehicle it BETTER WORK. I will order anything that will help monitor the important functions to me, going as far as adding stuff if the factory didn't offer. (Hey, never too many instruments; just look at a BUFF's instrument panel, or the flight engineer's station on a C-97. Always room for more...


)
I have concern about separating the circuitry in your plan as it causes the ammeter to no longer function as a system monitor. Yeah, the Mopar ammeters seem to flop around a lot, show hardly, if any charge at idle, but they do work as advertised. Where is the field signal for the alternator going to come from. How about the power for the voltage regulator. Will it be stable and adjust for usage, or will it be affected by a serial tap within one of the new paralleled circuits.
The BIGGEST concern I see is the use of the new power feed to supply the new fuse panel. You have a 40 amp quick reset circuit breaker. Are you sure 40 amp will suffice? If you add all of the available fuses maximum amperage the original fuse panel has listed you will find you are way under rated on your CB. Picture yourself having a great time running down the road at night in a heavy rain in the cold Texas winter, high beams on, wipers on high, defrost fan on high, optional fog or running lights assisting, and you unexpectedly come upon a tight corner, and tap your brakes. That brake tap may exceed your circuit breaker and quickly shut down the fuse pane circuits. This includes your ability see with the now darkened headlights, the wipers quit wiping, the ignition quits supplying sparks, the engine stumbles, the power steering gets hard (Armstrong steering mode), the brakes get to two footed operation, the pucker factor has exceed the fun factor...all due to a second or so of power interruption. Of course this may not happen, but with my luck, I wouldn't want to risk it.
With all of that said, I would attach the fuse panel in the same position as the old one. This would keep the ammeter working, address the overheated wiring that occurred over the years, allow you to upgrade your instrumentation, and keep you safer. You can split the circuits at the new fuse panel if you think you need to, but I would try updating in small steps by following the KISS principle and split from there IF excess heat is detected in any of the circuits.
Note: The heater fan motor is the usual cause for high current draw, which will kill the fan resistor and fan switch.
Ducking into the foxhole. Open for comments.