Update to battery not charging. It's going on the fouth week and all is well with the charging. The conole guage is always showing 14+ volts output even when lights and radio are on. A new high output Alternator had been installed and the NAPA battery was only a few months old.
Summary:
I found in another post that the alternator will not attempt to charge the battery "if" the battery voltage is less than 10 volts (My son had confirmed that the console gauge always showed 8 volts). The second red wire (10 gauge) that connects to the side of the alternator (in plastic clip) is a senor wire to tell the alternator to "charge" when it senses the battery dropping below 12 volts. Apparently, if the battery gets too low, it never tells the alternator to charge. I always assumed a alternator just "outputs" regardless. Anyway - based on that post I did the following stuff.
Tasks:
I removed the red wire (10 gauge) from the back of the alternator and replaced the connector with a new crimp-on lug. I removed the wire harness (clip with two wires) from the side of the alternator and removed the grime, tarnish from these clips and re-inserted them into the plastic clip and re-connected them to the alternaor. One of these wires is also a large gauge red wire (10 gauge).
I removed the factory harness cover and traced both the red wires from the alternator back to the firewall. Both of these wires are spliced (factory) together near the solonoid and then terminate on the battery side of the solonoid. The factory spice was removed. I cut back both wires, cleaned the ends and spliced a new tail (10 gauge) red wire to both (Y connection) and connected to the battery side of the solonoid. Only one wire runs from the solonoid to the starter. The small green wire connections were cleaned and reconnected to the small posts of the solonoid.
The battery was removed and slow charged/verified it was 12 Volts and re-installed. All battery connections were cleaned. The battery ground cable to the engine block was cleaned/re-connected as well.
A (10 gauge) ground was run from the battery negative and connected to the firewall. Paint was removed from firewall to ensure a good connection.
Fan belt was verified it was tight.
I checked the red wire (10 gauge) on the side of the alternator with the engine off and verified it read 12 volts (wire connects to solonoid/battery side).
Once started, the gauge on the dash showed the system was charging at 14+ volts.
I did have issues with taillights, turnsignals and dash lights not working.

I tried to walk my son through the process (on the phone) of pulling fuses to isolate which circuit might be causing a short or drawing current when the jeep was turned off. I had asked him to remove fuses one at a time while looking for a drain on the battery. I guess I should have also told him that the fuses needed to go back into the same spot! Anyway, once I put the fuses where they belonged everything worked just fine.
The old jeep is humming along and I'm hopping it will last another 25 years!
I hope the above information helps others out. It was getting very frustrating trying to decode the electrical drawings from the Haynes Manual. Tearing into the wire harness was much easier for me. I'm going to assume it was a combination of bad electrical connections and the battery having drained down to a point that the alternator sensor did not see a battery at the other end of the wire?