First and foremost, get some good schematics. The factory manual ones are not expensive and show the color codes. Also get a decent multimeter - they are not expensive - and a 12V test light.
The burning was a symptom, not a cause - so just replacing wires without finding the cause just complicated your problem.
DOT3 is a powerful solvent and can melt many plastics, including bulkhead connectors - and the bulkhead is where many, if not most, of Mopar electrical problems begin. Before I did anything else, I'd disconnect the battery and unplug the bulkhead connectors (if you can!) and *carefully* examine every single connection for signs of overheating or arcing. You may find it a fused mess. DOT3 is water soluable, so you can rinse it off.
My schematics show that the alternator's field winding and regulator get their power from the same point as the ballast resistor and ignition module - if you check you ought to see 12V at the center pin of the voltage regulator connector and at one of the alt field windings with the ignition ON. The alternator's BAT terminal ought to always be connected to the battery even with the ignition OFF.
I presume the car runs, so you've got power to the ballast, and hence likely to the regulator and alternator. If you do, then the alternator ought to be putting out voltage at its BAT terminal, but that's not getting through the bulkhead connector to the ammeter and from the ammeter back through the bulkhead to the starter relay and from there to the battery. Measure the voltage at the BAT terminal with the car off - it ought be 12V. If it isn't, you've no path to the battery, and with the car running it will likely go very high (up to 50V), but the current can't go anywhere.
In that case, you very likely have damage at the bulkhead pin J and/or P. These are often trouble points. The connections right at the ammeter also are prone to give trouble. *Do not force the nuts off*, you'll just break the ammeter - if they don't unscrew easily, cut them off carefully - I use a Dremel #409 blade.
Once you've found the problem, you can address it several ways. If the damage is limited to just the P and J pins, you can (1) bypass them entirely just as the factory did for the HD charging systems, or (2) find a donor harness and fix your harness properly, or (3) buy a reproduction harness. If the bulkhead is badly damaged, go with (2) or (3).
If you decide to fix your harness, I strongly recommend you remove it from the car, taking notes as you go on how it was installed, and fix it out of the car, then put it back. The underhood harness is pretty easy to remove, the underdash more difficult. Some people remove the whole dash assembly as a unit, others remove the seat and work from under the dash - either will work.
If you got much DOT3 in the bulkhead, you'd probably be far better off fixing it entirely and properly now, rather than wait for
subsequent problems. You can unclip the pins and wires from the old bulkhead housing and transfer them to a new housing one at a time. If it's melted, you can use diagonal cutters to cut away plastic until you can extract the pin and wire. Chean and inspect each carefully as you go.
The secret to a trouble-free electrical system is to treat every connection as if your life depends on it - barrel crimps are just for emergency repairs.
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My sons 73 duster (slant 6) had smoke from under the dash on his way to school. I found and replaced a section of 12 guage black wire just inside the fire wall on the inside of the car. Also found the same wire burned at the quick connect in the engine bay just behind the valve cover. I straight wired it to bypass the connection. The problem is im not getting any charge from the alternator now. I replaced the alter. and the voltage reg. and still no charge. amp meter shows nothing and the engine will kill when the pos battery cable is pulled. Im not skilled in electrical areas so it may be simple fix but im stumped. Any suggestions before I take her to the doc??
Here she is w/my son. little less than 40k original miles.