By shutting down, do you mean it actually stops running? Is restarting easy? Any noises or rough running immediately before shutdown? Any black smoke from the exhaust?

You seem to have two problems (1) Your speed is low for the amount of RPM, so the first thing I’d check is if your tachometer and speed measuring are accurate. (2) Shutting down. The vast majority of diesel engine issues are fuel delivery related. Either not enough fuel, air mixed in fuel, injector pump/timing, faulty governor. Some basic sanity checks for #2:

• Engine stopped, transmission in neutral. Rotate the prop shaft. Rotate freely?
• Engine stopped, key switch held in preheat position. Do you hear the lift pump clicking?
• Engine stopped, disconnect the fuel return line at the engine, key switch held in preheat position. You should observe a bit of flow.
• Where you disconnected the fuel return line, blow into the fitting that goes to the engine. It should be clear.

Air getting into the fuel may yield similar symptoms.

Ahhhh.  Forgot the tank might be developing a vacuum if the tank vent is clogged and thus starving the lift pump.  This seems like a very likely suspect given the sputter/resume behavior.  Might try running with the fuel filler cap unscrewed enough to act as a secondary vent and see if this makes a difference.  Your tachometer jumping around can be a "normal" artifact of your batteries at full charge.  When it starts to jump around, go turn on all your cabin lights plus your exterior lights and see if this changes things.  I still suspect your speed vs. tachometer reading is not correct unless your boat hull is very fouled.

Has your boat speed vs. tachometer always have this ratio or is this something new/recent?

I had the exact problem and did what you did... changing the filters. Turned out the fuel line into the primary water seperator fiilter (which makes a 90 degree turn on a fitting) was clogged . The filter never got a chance to do its job. Try cleaning that out as its the simplest thing to try.