People really give electrical systems low priority on their vehicles...until it finally kills the vehicle.
It sounds like you have a lot of sorting out to do. You can start by checking the voltage at the batteries once you get the truck running.
If the voltage is around 24v, the batteries are not charging. You should see closer to 28 volts while the truck is running.
At this point, there are 2 possibilities:
The generator is dead or the wiring between the generator and the batteries has been cut.
Next step: Put the meter directly on the generator leads and check the output while the engine is running. Use CAUTION around the spinning belts and fan! If you have 28 volts, the generator is charging properly, it's just not getting to the batteries and you need to find the broken wiring. If you have "0" it's obviously dead. If you have in the 20's, but less than 28v, it could be as simple as adjusting the voltage regulator output.
As for killing new batteries within a year, you may have a short to ground that slowly drains the batteries. To test this, connect the batteries and put your volt meter on them and carefully watch the voltage over 15-30 minutes. Do NOT start the truck. If the voltage starts out at 24.98 (for example) and it continually drifts lower without ever settling out, then disconnect the negative cable and observe for another 10 minutes or so. The voltage may actually rise a few points, or at least stop declining. If that happens, you have a minor short in the truck wiring.
In general though, it's not good to let the batteries sit for a full year without occasionally topping them up. Either buy a 24 volt battery tender, or buy a pair of 12v tenders and remove the interlink cable between the batteries.
Regarding all the cuts in your wiring harness, there is a complete wiring schematic in the 5-ton manuals for your truck. All the wires have tiny, metal numbering tags on them. Read the number, trace it to the number on the wiring schematic, locate the wire on your truck and splice them back together or replace the harness altogether.
You can grab that manual, here:
https://www.steelsoldiers.com/threads/tms-for-the-m39-series-5-ton.77614/
It's tedious, but not difficult.