Putting it all together here is my two cents worth. If you (maybe) overheated the engine I find it incredible that you had an event that resulted in the fuel
system (pump or governor) being changed that would show up for 10 mins and go away. If this was my project
I would verify the exhaust
was NOT restricted in someway. Then verify the valves were adjusted to spec. Then check the injectors all ?GM injectors are easy to clean and inspect. just "You tube it"! I had a 1GM that finally came down to pulling the head
the problem was the exhaust
seat after 25 years was just shot it smoked for 10 minutes then cleared up on heat up. Yes it cost some boat jewelry $$$$, but a new head gasket
and new head and a few hours no black smoke the power is back. Just start at the top and go backwards. these engines will last for years unless you are using them everyday all day most don't have that many hours on them. Do the simple stuff diesels will take some abuse. Kiss it "Keep it simple"
Diesels need 3 things (air fuel and rotation)