Diesel Bombers - fuel bowl ran empty after a fill up

After rebuilding all 8 injectors, I was hard running the truck to get the air out....was running better but started throwing a CEL code after getting on it for about 12 miles, shut the key off and back on, code went away and then did the same after 12 miles or so. Last night, I was down to about a quarter tank so stopped for a fill up. Got only about 2-3 miles (in the middle of nowhere of course) and the truck suddenly just stopped running, would not restart. I opened and checked the fuel filter bowl and it was empty. After cycling the key several times, I did get fuel back into the bowl but it never did start again. After three hours, I did get a tow to my local mechanics shop. Went today to try and start it and now the starter is dead...guess I may have killed it by trying to crank it so much last night. Any thoughts on why the bowl would run dry? Also, when my local parts store tried to put their actron code reader on it earlier in the day yesterday, the truck would shut off as soon as he tried to run a diagnostic....I figure that code reader was doing it. Any one had a similar issue on any of these points? Just want my truck to be running again.