There are several reasons that I can think of causing a boat to make a sound like the one you have recounted but to have it reoccur 2 more times the same way narrows down the field a bit. You narrowed down the field even more by discounting other ideas. This only leaves 1 answer which..... no one seems to have come up with yet. The Engine.
I have a Hunter 40 with the 44hp Yanmar engine. It occasionally makes the sound you have explained while I am motoring. Never to the extent you have reported but I can see how it could happen.
Here's the problem. Your diesel engine was either Knocking........ or backfiring . These are two different problems with a similar sound. I can't tell you exactly which one yours is doing, but I will give you some reasons why either happens and you will have to check to see if the problem exists in your engine . It may be any one of these or a combination of them.
First you must understand what the word Octane means.
http://en.wikipedia.org/wiki/Octane_rating
(VW Passat diesel engines have had a similar issue but lasting much longer. I almost bought one but backed away when I restarted the engine after the test drive and it started rapping.)
http://www.fixya.com/tags/knocking_sound_engine/browse/volkswagen
Here are some possible answers:
1) The red marine fuel makes my engine knock or backfire..... don't know which, but it sounds like a gun going off under water and hitting the boat making a kind of muffled pinging sound. I guess the red fuel has either a little lower or higher octane rating. This makes the fuel harder to burn so it fires early or late. If I were to put regular road diesel in the tank I think it would stop......... Yah ahhhhhh....... it might fix the problem....... to bad I can't try it because that would not be legal. Do you use Marine Diesel ???
2) When your boat got all stirred up in the weather, so did your fuel tank. The crap in your tank, (diesel bacteria, water or unmixed diesel additives) will float up and get sucked into the engine, raising the octane level and causing backfiring .
3) While your boat was on it's side and with the fuel line or filter clogged the engine temporarily burned its own oil.......which I assure you can happen. Engine oil has a much higher octane level so it might cause backfiring.
4) Did you accidentally put a little gas in your diesel tank ?? They do mix but some gas may go to the top. This will cause the engine to pre-ignite or knock. Eventually it could self destruct.
5) The main heart of your diesel engine is the injector pump. in a modern 4 cycle diesel engine the pump must be timed to squirt the fuel in at the exact time. To early or to late will cause the banging. If dirt gets into the pump it will slow down causing the banging. I'm not sure but I think there is a sort of advance on the pump, like the vacuum advance on a cars distributor. It's purpose would be to pre-pump the the fuel when the engine is running at high speeds. If this didn't happen, you could get the banging.
It's only a theory..... I broke my leg in HS so I missed this portion of auto-shop.
6) Lastly.....135 degrees is to cold for a Diesel engine to run. If the glow plugs are to cold or to hot this would cause the engine to fire early or late.
I believe one of these two, early or late ignition are causing your problem. If I am correct, and the symptoms continue, left unattended, this will take your engine out. Treat this as a serious problem, you need the engine to work under extreme situations. Find a very good mechanic to truly diagnose the problem.
Of course this is only a theory...........
Good luck,
Tom