Hmm, sorry I've run out of halfway decent ideas, but hopefully someone with more knowledge can comment. I bet you could get a voltage reading off the ecu, but I'm not sure what it should read or if that by itself would yield helpful (since you were able to check codes I'm guessing not). That does remind me though I should probably put a new battery in mine for the winter :)
Probably doesn't matter, but is the truck a 5-speed or auto? Also I'm assuming the fuel filter is fine since you did the pump also.
Also does it seem to run all right once started?