Just so that everything is clear, have you bled the high pressure lines up at the injectors on top of the engine? You have fuel getting to the pump, if you can confirm there is nothing getting to the injectors, then either something in the pump internally is holding the fuel control off or something has happened to the high pressure pumping element. I myself am fairly new to this specific pump, but I understand there is a 'button' on the bottom of the pump plunger that can fail/ come off and not allow the pump to travel its full stroke and build pressure.
From here it is looking more and more like a Head problem. Yep other than leaking O rings that dang button problem has showed up way to many times. Now on the bleeding of the injectors when all is right we do not need to bleed the Deuce injectors if we just run out of fuel. We do use the bleed screw between the final fuel filters after a filter change to help get the air out faster. For just checking for a problem I like to leave cracking the injectors till the last thing before I pull the Head. I only say this as some injector lines have been on for 30 years and have seen more than a couple of times damage to the tips on the fittings. Believe this happens when the tip of the line get seized to the injector. The metal to metal binds up and can knock a chunk off the sealing area on the line fitting. This will not seal and cause us to buy / find a new line. Yea sometimes we have to remove all the injector lines to R&R the Head. I see where he has already cracked some lines so we will see if any damage was done when / if he gets it running.