Our Ford Powerstroke 7.3 powered wheelchair van's battery issue

     Last night I go to get into our truck to go home about 10 pm in the rain. and the truck would only turn over slowly but wouldn't start.  It's always the coldest wettest nastiest time of the night when your vehicle fails.  I'm still fortunate in that I still have people to call who will help me out and come out on the nastiest nights and give me a jump.
     This last fall I replaced both batteries, yeah powerstroke diesels require 2 batteries, with Sears Diehards. And things have been good in the battery department ever since but for some reason last night the truck won't start, the batteries had gone down.
     On the Ford Powerstroke van one battery is in the engine compartment, the 2nd battery is on the passenger side frame rail just behind the front door. This 2nd battery is always the fun one to work with as you have to lay on the ground to get your hands on it.
     The International Navastar Ford 7.3 Powerstroke Diesel is a battery hungry machine.  It has eight glow plugs, one for each cylinder in the motor, that fire off for a brief time prior to starting and run for a brief time after starting.  The glow plugs are tied straight to the batteries with a heavy relay as they pull approximately 180amps when they are on!  The starter on the powerstroke is a gear reduction Mitsubishi starter that pulls anywhere from 400-600 amps when starting. This is why there are 2 batteries as most single automotive batteries have a CCA (Cold Cranking Amps) rating of about 800 amps max meaning with a single battery the powerstroke will just just melt one down pretty quickly as it's almost like the battery was at a dead short. So they put 2 batteries on the truck giving you 1,600 CCA which should be more than enough to give you enough power and reserve to start the truck on the coldest mornings.  But theres a 2nd issue with the 7.3 powerstroke diesel and this ones important to remember. Just because the battery has enough power to physically turn the motor over, if the motor doesn't hit 100 RPM the injector module will not fire the injectors to give the motor fuel. This is where I was last night, the truck would turn over but slowly and it wouldn't hit a lick (to use an old colloquialism.)
     I go out today to start it figuring it would have been fully charged up from the alternator on the ride home last night but the batteries are dead again. So this leads to three possibilities:
     One is hopefully they are just dead, I put the charger on it today and they are charging, this theory is based most likely in fantasy.
     The second possibility is that one or both batteries are bad or low on water. If anything is wrong this one is my hope as the batteries are under warranty and this will be an easy fix. Albeit the batteries are very heavy large batteries and one is not in the easiest place to service
     The third and most dreaded possibility is that there is a short in the wiring. This one scares me to death as I have had zero energy for quite some time and am unsure if I can find the motivation to chase this down.
     Today it has been raining all day. and the temperature outside is 43 degrees F at the moment. You add to that the fact that I'm dealing with a sinus infection and you can see that I have no business being out in the weather to work on it.
     If anyone has any suggestions please post them in the comments I'd love to hear from you.