I wish I could help you more, but I'm not really a diesel expert. By coincidence I ran my (diesel) tracked loader out of fuel just yesterday for the first time. It was facing uphill so I had to put 20 gallons of diesel in the 30 gallon tank before it would bleed fuel from both of the fuel filter canisters (the filter canisters have air release valves on the top of each one). After I bled the air from both filter cans, and had a decent amount of fuel running out of the vent valves, I then cracked the inlet line going to the pump. I opened it fairly well too, not just barely cracked. I could see bubbles and air coming out along with fuel. I kept bleeding it until all I saw was fuel and no more air bubbles. Then I cracked three of the six injector lines (where they go into the injectors themselves), and turned it over a bit. I could see wetness around one of the loosened injectors while cranking it, and then also heard it sputter just a bit. So I tightened all of the lines back up and then she fired right up after that.
Are you sure this machine only has run out of gas and it's not something more serious? Also running it for a few moments on ether (starting fluid) may help to get it going, but I've heard mixed things about using ether on diesel engines (i.e. some say its ok, others say its not, but everyone says a lot of the stuff is BAD).