I worked on it again today with some fresh diesel. I put some water-remover in last night, and let it set overnight. I had the 3/8 in clear tubing running from the diesel can up to the lift pump, and then stuck some more 3/8 in tubing in the 90deg hose on the pre-filter and let it drain into the same diesel can. I started the truck up (or starting fluid) and it ran for about 10 minutes until I killed it, with fuel being pushed from the supply line into the diesel can, mixing the year-old fuel with the new fuel.
I then ran the 3/8 in tubing from the pre-filter to the lift pump (I wasn't going to try fighting with that 90deg hose again). I manually primed, and then started on starting fluid. Again, it was running fine, on year-old fuel. I hope this means the water-remover worked. I put the intercooler hose back on the intake manifold, and again let it run for about 10 minutes until I killed it.
I decided to see if I could start it a third time, this time without starting fluid. No luck. The engine would spin, but not even act like it wanted to fire. I don't know if the battery was just weak from earlier, or if something else is going on. Also, I noticed that the vacuum line that goes to the power steering pump has pretty much disintegrated. Autozone just tried to give me a rubber hose. Is there a local source for vacuum lines, or is this something I need a Dodge or Cummins number for?