Updates: first D2 Cat, you da man for eBay! The shop manuals all 5 volumes, each roughly 2 inches thick just arrived in the mail today, and they would have been extremely helpful, detailed trouble shooting flow charts, with fuel line pressures etc. So I am ready for next time, ready that is to have available to a qualified mechanic
The guy that worked on it stopped by yesterday for a down payment ($4100 for the parts). and we had a long visit about the logic of it all and where the troubleshooting went wrong. The experiment that threw a red herring was one in which he detached a fuel supply line and substituted one that went to a jerry can with fuel in it that was setting next to the truck. Prime it with the little manual pump near the engine and it would run perfectly for 45 sec and quit. So he concluded that the supply pump built into the high pressure pump was no good, and replaced the combination. New pump it ran a little longer but rough and some smoke, so concluded bad injector. Replaced injectors, still wouldn't run more than 45 seconds. By now he had clear lines in various places, not sure when he saw foam in the clear lines, but eventually he put the jerry can up on a ladder and ran a supply line to just before the fuel filter, and lo and behold it ran for 45 minutes just fine. So he pressurized the fuel tank and found evidence for a leak in the line near the tank and the fuel cooler. Replaced fuel lines and fuel cooler and it ran. Poor guy said he could have laid down on the floor and cried when it finally ran!
So the thing that neither he nor I can understand is why that first experiment with a line to a jerry can next to the truck didn't give a meaningful answer. If it had run then he could have skipped replacing the pump and the injectors, and kept on looking for a vacuum leak, which was high on everyone's list as a possible target. We speculated there might be some pressure thing going on that was absent in an open fuel can. The way he had it set up the return line from the common rail was still dumping leftover fuel back in the truck's tank. I guess either that or something sloppy about how it was set up. Not sure how much fuel would get pulled into the test line during the manual priming process, so it wouldn't break the siphon when it was running.
Well this has been quite the learning process...still wondering how the first guy came up with the idea that it was injector no. 2.