The brake and CTIS lines are clear, obvious and not the ones in question
"Each axle should have a vent line to the top of the axle housing.
There should be the control air line to the power divider on the intermediary axle differential(AWD to 6WD control when mode/6X is selected)"
Here's a picture of the intermediate axle:
The smaller air line toward the top of the picture, near the U-Joint, must be the control line that locks the axles together. The larger, toward the middle of the picture, on the square part of the axle is the one that goes to the rear and ends in a 45 elbox, shown here:
The air line coming down from the top of the picture to the T is the one that comes from the square portion of the intermediate axle, continuing down from the T it ends in the 45deg elbow shown at bottom center of the image.
That elbow has pipe dope on it, it was obviously connected to something at one point. If it's a vent, then aside from being a loose uncontrolled hose, it's probably not doing any harm.
If the brass "cap", vertical center right of the image, that rotates freely is a vent, then maybe removing the loose line, capping the lower side of the T and letting this line vent through the "cap" vent might be the play?
I am very curious to know where that 45 degree elbow was connected. There's no obvious empty or plugged place to thread that in.
I've not yet had the occasion to push the MODE button on the Allison shift panel, so I don't know what happens at that 45 elbow. I'll get the truck out of the garage, get someone to press the MODE button and see what happens back there.