Jaime,

In your response (#17) you said at no time did the voltage ever read over 12 volts.

In a healthy system the voltage should be between 11 and 12 immediately after it starts, but then it should move up to over 13.5 after a minute or so (when the glow plugs turn off).

If this does not happen, this means either your batteries are seriously drained or the alternator is not functioning correctly, or, you have a serious short somewhere.
Sorry for re-stating the obvious, because I know you have been looking at it many times and it must be getting frustrating at this point.

If you're ready to start searching for a short, here's how you can do it without starting the vehicle.
Put an amp meter on one of the battery ground cables (the driver side is a good one to start with) and note the current.
Testing voltage is not much benefit because the voltage will not show much instantaneous change when you remove the short, since the battery is such a strong source.
Leave the amp meter connected and start pulling fuses, one at a time til the amperage goes down. If the amperage does not go down after pulling one of the fuses, put the fuse back in before moving to the next one. This way you'll only have one fuse removed at a time.
You can buy an amp meter that has an inductive pickup, which makes checking current easier. You could also buy an amp meter that uses a shunt, which you must connect in line with whatever circuit your testing.

Once you find the circuit (fuse) that's the culprit, look at your owners manual for what the circuit is. In most cases, the vehicle will start without the fuse installed. You can then re-charge the batteries and then start the truck. This may enable you drive the truck while your narrowing down the exact problem.

 

Bustedknuckles,

Thanks for the big help I'm so ready to get this problem solved already very frustrating. The system has never gone over 12v after start or even after glow plugs turned off I guess the reason would be due to a short somewhere. Would I need to charge the batteries again in order to check through fuses or would fuses test out either way I knw you said its not much benefit but at this point to me its a next step I've been stuck at just pulling the batteries out charging them an pulling the alternator out an then back to square one. Ill get that done an let you know what I find.

 

Jaime,

We need to take this a step at a time.

First of all, I did NOT say that checking for a short is of little benefit. I said the opposite, checking for a short is the first thing you need to do at this point. Whether your batteries are good or bad, you need to know whether their is a short.

Do you have an amp meter?
If so, is it an inductive type or a shunt type?

If not, get an amp meter. The best one to get is an inductive. It will cost you about $65.

Here's one from Amazon($61; including free shipping):


If you want to proceed, I'll continue to help you.
Let me know when you have the amp meter and are ready to proceed.