Getting air to the trailer gladhands requires the truck controller brakes off (yellow knob) and also the red trailer controller enabled. Be sure to have chocks under the tires because the truck will roll otherwise! This is a terrible way to have to use to get air for tires.
I have seen a situation like yours, where the tires get deflated and will not re-inflate, and the CTIS controller faults out. The CTIS controller gets confused, I think because the front and rear axle/tires get deflated to unequal pressures. Why? Possibly because there is a restriction in either the front or rear quick release valves allowing the faster 'dump' to drop pressures faster on one axle (one QRV on each axle). Then, when the system makes the dump, stops the dump and measures pressure, it sees a changing pressure. That is because the front axle and rear axle are at different pressures, and when the 4 wheel valves get their 15psi-to-open signal, there is flow from the highest pressured axle to the lowest pressured axle, trying to equalize. This test does not last long enough to allow equalization. As the CTIS controller tries to measure the system pressure (and it only looks at one combined system pressure) it sees change and thinks there's a bad leak and shuts down.
You can verify if your axles/tires are at different pressures with a manual gauge. If so, inflate the two tires on the lower pressure axle to match the higher pressure axle. Now the CTIS will not see changing pressure and may take over and work. [edit, it just occurred to me that lowering the two higher pressured tires to match lower pressured tires would achieve the same equalization goal, and does not require hooking up the air hose]
Sounds like you will need to go through your air system looking for bad components. Not a trivial job hour-wise, but not too expensive a repair. Lots of threads on here about CTIS and air system components.
My opinion of the highly-structured trouble-shooting steps in the manual: designed for someone who will not have any idea of the theory of the system, and has unlimited time to blindly follow troubleshooting steps. Hope we are beyond that. We FMTV owners had better understand our trucks or you will undoubtedly get stranded somewhere. A little knowledge of the system, and normal human logic, will allow so much better troubleshooting than the manuals 'brainless' test steps!
Bob