I was taught that automotive alternators need to be connected to a battery. If you disconnect a running alternator from its battery, you can fry the voltage regulator or worse.
Search the site for info about eliminating the DUVAC from your system. The DUVAC was a really bad idea. There are several approaches. I went with the "Plan B Mod", but a smarter play might be to go with 2 12V alternators, one per battery. I'm not sure my 2 voltage regulators are playing nicely together. I'd need to install shunts and ammeters to find out. Haven't opened that can of worms yet.
My M1010 thread is here, FYA:
http://www.steelsoldiers.com/showthread.php?135493-M1010-for-my-daughter-the-field-biologist
Battery drains are tedious but straightforward to figure out. You follow the circuits from the + post on the battery to the - post. Something in there is allowing electricity to flow. It's a simple process of elimination. To measure electricity flow, I got a clamp ammeter, and clamped it to the wire connected to the + post. Remove fuses and disconnect things until you have little enough current flowing that you can use an ammeter. Disconnect the + wire from the + post on the battery, and put your ammeter in the circuit. Mine handles <0.1 amps. Be careful you don't fry yours with too much current.
If you pull all the fuses, and turn everything off, you should see no current flowing. You may have to disconnect your alternator. Some leak current. Once you have no current flowing, you can re-connect things one at a time until you find the one that's allowing current to flow and draining your battery. You'll likely find a few things that are at fault. Cracked insulation on old wires, leaky diodes -- lots of possibilities. Turning the main light switch off is good advice. So is a trickle charger when the truck is not in use. I do both. I also have a small solar panel. All of this is discussed in detail elsewhere on the site.
While you are doing this, take the time to clean all your electrical connections and grease them with dielectric grease. I like no-ox-ide, but there are other good products out there. Again, this is discussed in great detail elsewhere on the site. Old connectors with corroded contacts can cause intermittent electrical gremlins that can be hard to track down. Clean and grease every electrical contact/connection, as you work your way through the vehicle.
I find most any question I have has already been answered on the site. Search, read the M1010 & CUCV threads, and you'll find most questions answered without your having to ask.