First, did you also change the secondary filter on the engine? Here's a post that shows its location (for turbo engine, but yours probably similar):
https://www.benzworld.org/forums/w124-e-ce-d-td-class/1419818-1995-e300-diesel-fuel-filters.html
Also check the filter that you cleaned again -- if it's dirty, that means rust or debris from the fuel tank or fuel line is coming loose.
If you can access the fuel pump (usually inside the gas tank), they often have a flexible mesh filter to catch big stuff that can be removed and cleaned (or replaced, if there are holes in it).
But if the problem recurs, you'll probably need to remove the fuel tank and get it "boiled" to remove the rust and other stuff. And you might as well replace the fuel line, while you're at it.
Finally, a bunch of gunk in the gas tank can definitely shorten the life of the fuel pump, especially if the mesh filter wasn't capturing all the debris.
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