I don't think pumping the accelerator is going to do anything to help you start your car except maybe make you think you are doing something useful. Unlike gasoline cars there is no accelerator pump in a Diesel system, so you are not adding any extra fuel by pumping the acclerator. Still it does no harm and probably makes you feel better.

I had the same problem with my Chevy 6.2 Diesel. I found a small leak in the line from the tank to the pirmary filter. The filter was above the level of the tank so when the truck stopped the fuel would slowly syphon back to the tank. A tighting of all hole clamps and fittings solved the problem.