Engine Mechanical problem
1990 Ford F350 6 cyl Two Wheel Drive Automatic 98,000 miles

For my business, I have an old uhaul box truck that I am running on biodiesel and diesel. I accidentally ran out of fuel 2 weeks ago. I was able to get it to start again and it started just after I got it home. It did not start the next day, however. It was giving a "water in the fuel" message so I opened the valve and let the water out. After several tries to start it, it would rev and not turn over. After several tries, it seemed to be losing power. I then jumped it and tried to start it. Still no luck. In fact it seemed to be getting worse. My next plan is to replace the fuel filter and bleed out the air. How do do I bleed out the air on a 1990 Ford F 350 diesel truck?
Do you have any other ideas for it?