That doesn't sound good... Since the injection pump elements are lubricated by fuel, it could be that they were damaged when the fuel ran out.

I can't think of another reason why output would be bad on just those two elements, other than the (remote) possibility that there is still an air bubble in the fuel gallery. First thing I would try is to make another effort to purge any air from the fuel system with the hand pump, perhaps cracking the banjo bolt on the IP return as well as the banjo bolt on top of the fuel filter (just make sure fuel is leaking out, i.e. under pressure, when you tighten them).

Also, if you post this in the Diesel Discussion section more people with the relevant experience will see it.

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99 E300 Turbodiesel 100k