Have you checked to see if the diesel tank vent is clogged? After it stalls out, get out and open the fuel cap and if you hear air then the vent is clogged. That's the only other thing I can think of that would cause this. It can't be a fuel issue, because if it runs on veggie, then it's got to run on diesel. You aren't running with the fuel lines under vacuum with your setup, so I doubt there is air getting into the lines. Although there is one other possibility, that the injector return lines are cracked and somehow allowing air into the system, but I am not sure how that would happen because it doesn't look like you have a looped return, but it wouldn't hurt to change out those lines if old.

__________________
87 300D - Running on Veggie oil; 260,000 plus miles; Original #14 head