When a diesel runs like you describe and the filters and fuel flow are ok, I next suspect that an injector is clogged. With the engine running, one at a time loosen each fuel line where it attaches to the injector to relieve the pressure and see if the engine slows/lopes. The one that makes no difference is the one that is clogged.

You will be working with very high pressure fuel but in small quantities, take precautions. This procedure is listed in many places on this forum if you are not clear, search. Good luck.

If you loosen the line on #5 and no fuel leaks, suspect that you caused a problem as you mentioned earlier.