Reading back through the thread, I did not try using the block heater, and I did not try disconnecting the return line on the top of the pump but have tried everything else. I haven't had time to work on it again yet but I'm planning to do that Friday.
There was only a small amount of white smoke out the exhaust, it's definitely not as much as you would expect.
The water seperator was replaced with a Racor one that had a plastic bowl on the bottom that was there when I bought the truck. I replaced the filter, but everything I have tried to get it started has been with an electric pump connected to the line feeding the fuel filter and still had no luck.
If the injection pump did fail, would it be normal to have it go from running fine to dead within 30 seconds? I am beginning to think that's what may have happened, but I also don't want to swap the pump just because it got air in the system and I don't know how to get it out and there was actually nothing else wrong.
I don't even know if I want to keep it anyway, I have put a lot of time and money into it but I don't think I have the ability to get the fuel system sorted out enough to be drivable, and if it's just a project to spend every weekend working on and never actually use I could get something that's less stressful and frustrating. I did drive it from near San Francisco to LA twice and it was fine then, but it's obviously far from being reliable enough to try that again.