Fred, if you can pull this off, you will be my eternal hero. Seriously.
My thoughts: as soon as you want to include items swimming under water (torpedoes, Mobby Dick etc.) you will need to use resin. There is simply no way of convincingly attaching these items to let's say the back wall of your diorama. So you will have to pour layers of resin, placing all under water stuff as you go. This is going to be a slow process, as you can pour the resin only in thin layers to prevent it from overheating. Companies like AK Interactive started selling products for creating water, but I am not sure if these products are suitable for the depth you need.
With an infinite amount of patience, you will also be able to recreate the effect of distorted water behind the torpedo, as well as the ships wake.
As to spinning props, in this scale you might get away with clear plastic discs and some airbrushing to get a prop blur effect.
Animals. I think making your own fish is quite possible. Again, in this scale there is not too much detail, so I would just give it a try! I'd suggest a two-part epoxy putty like Miliput Fine, or - even better in my opinion - Green Stuff.
I hope this makes any sense, if you have any questions - shoot!
