You might be looking at a clogged fuel filter or pre-filter.

Also, I had a gasolene vehicle do similar things when I let it stay outside one winter with 1/4 tank of gas. Water condensed inside the tank, and as I got to the bottom of the tank it would hardly run. Upon filling back up it ran fine.

Of course, with a gas tank you can add the alcohol-based treatments. Not sure that's a good idea with diesel. Search my thread on diesel fuel additive label scans (under my ID) and see if anything there looks appropriate to remove water.

Ken300D