Hit the nail on the head. Whenever you run out of diesel, if you are not working with a full tank afterwards, you are just asking for trouble.

After all you have done, you are just going to have to pull the line after the fuel pump, and then turn the key on until the pump starts sucking diesel. Once you have diesel coming there, hook the line back up. Make sure you have the cap off the fuel bowl and turn the key on again to make sure you have fuel coming up to the bowl. If you do, she'll start.

If not, you are going to have to get some air to blow in the tank while you have the pump running and checking the fuel bowl for diesel.

I have helped several friends get their trucks started after running out of diesel, and always get them running. If you would have just filled up the tank to begin with, 9/10 she would have started right up.