I'm having somewhat similar issues with my '95 - unfortunately - I found my wiring to be original and horribly falling apart - I've now rebuilt 3 harnesses and I think I've gotten all the bad wiring replaced. I sent my injectors to Bryan who thinks they are originals at 265k and they are in serious need of new nozzles - so - you might consider having your injectors checked as well. I'm replacing the DV seals, rebuilding the fuel pump and replacing the lines "while I'm in there" my intake manifold did not appear sooty so - I'm wondering if previous owner already plugged the EGR - or if it just doesn't work any more.
Hopefully sometime around Mid January I'll have all the parts in hand so I can finally put this thing back together again and see how it runs. Hopefully I'll have a glowing report!

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95 E300 Diesel 265k and counting