Help me diagnose charging issues 2006 ram diesel

So, im diesel stupid. 

Dads 2006 dodge ram 2500 with a Cummins. 

Had battery light on, took to oriellys and tested alternator. Bad alternator, so.i swapped it. 

Still having charging issues. Dash reads about 10v, passengers side battery 17.5 at idle, drivers 11.5v

Apparently its a computer controlled alternator, not internally regulated. 

I have no freaking clue what im looking at here, and my Google-fu is weak as hell. 

Can someone lead me in the right direction?

I've had one bad battery take out the alternator on my '01 with a Cummins. Disconnect the pair from each other and test them individually. If you can let them sit for a while before testing that is better.

There is something desperately wrong with a battery or the cables.

What he said.  The alternator sense must be connected to the driver side battery and there must be a connection issue between the two.  At 17.5v clearly the alternator has output but it is not making it to the other battery.  They run the batteries in parallel so I would focus on checking for a voltage drop between the two positive terminals and the two negative terminals. It should be a tenth of a volt or less.  One of the two is going to show you a six volt drop, that will be the thing to focus on.

I just did an engine in a Journey and it was setting a code for the current sensor in the negative battery cable. Of course anything wrong with the car would automatically be our fault so I went ahead with diagnosing the issue.   I removed the airbox and found this.

Given that the alternator is charging, and the whole truck system is showing low voltage, I bet that the issue is the positive cable connecting the two batteries together.  This would be proven by putting the voltmeter leads on both positive terminals, betcha it will read six volts.

Yall made me do more checks. 

I put jumper cables between the two batteries, and they stabilized in voltage (1.1 volt difference). This was repeatable. 

Having this led me to  believe that the crossover cable has failed, which apparently is fairly common on these. 

I have one on order.

What else should i look at, or did my diagnosis provide a reasonable explanation?

If the two batteries are at such different voltages, they must not be connected properly. It sound like your diagnosis is not only reasonable, but the only one possible.