Changed the fuel lines from the water separator to feed pump, feed pump to fuel filter and fuel filter to injector pump plus the return line. After bleeding the lines, machine started right up. Did some other maintenance on it, then went to work. About 30 minutes later it died, we are back to the same routine crank for a bit, machine eventually starts, then looses power and dies. FYI - Friday I had a fellow that maintains equipment for the contractor working on our house look at it, he was the one who reported air bubbles when he cracked the nut on one of the injectors, had him replace the fuel lines since my day was pretty full.
Assuming air is still getting into the fuel system seems like the options are limited to the water separator and the pickup tube in the fuel tank. So this AM I started with the pumpguysc's suggestion and removed the bolt in the banjo fitting on the fuel line feeding the injector pump to inspect - clean as a whistle. While I had this apart I turned the key to "run", which started the feed pump. No fuel came out, no air, nothing. Obviously a problem. So I broke the suction line at the input to the water separator and put a little pressure on the fuel tank - fuel came pouring out, don't have a blocked pickup in the tank. Next I took apart the water separator, it was a cruddy mess with lumps of black stuff filling the bottom and a messy element. Good to find something, cleaned it up, blew the crud out of the pickup tube / bolt and tried to find a replacement element. We live in a very rural area in the Bible Belt, so finding something like this on a Sunday was not successful. So I cleaned everything up, blew the large lumps off the filter element and put everything back together. Cracked the bleed nut on top of the separator, put a little pressure back on the fuel tank, drove the air out. Put the key back to "run", now fuel pours out of the line feeding the injection pump. Buttoned things back up, cranked the engine and she fired right up. Loose crud floating around in the water separator bowl may explain one of the early symptoms, where the machine would die when driven up slope. Will order a new element, and also replace the spin on fuel filter, concerned that some of this crud may have migrated to the filter.
Interesting note that the manual lists draining the water separator as a 50 hour task, but there was no mention anywhere on replacing the element in the water separator, it wasn't even listed on the consumable parts list. Makes one wonder if it had ever been replaced. What was the black crud - algae? I run ultra low sulfur pink diesel with an algae inhibitor.
Thanks for all your suggestions, I am a real newbie when it comes to mechanics. This would probably be a trivial problem to you veterans out there, but it forced me to learn more about my machine. Now to figure out why the temperature gage has stopped working, the fix a leaking seal on a final drive.