Tried actually to get the Japanese Midgets to work in SH2 but they always seem to crash the game when they roll over. I think they might need to be permanently submerged LOL. The bigger ships seem okay but unexplained crashes happen now and again.
That being said there's a good book called SUNK by a wartime sub commander, Hashimoto, I think he sunk the USS Indianapolis or something about the IJN sub fleet. It would be an interesting mod I think or if they ARE going to the Pacific, at least let us play not just the American side but the other side as well!
The Japanese had a very sizable submarine fleet but they were not well directed tactically, prioritizing warships over merchants. But they could have good missions - the midgets particularly (infiltrate Pearl Harbor on Dec.7, the Sydney Raid) and could even explore such flights of fancy as the Panama canal raids or what if the USS Indianapolis was sunk delivering the atom bomb?
Here's a good set of missions to start with!
http://www.ww2pacific.com/japsubs.html
Enjoy,
Mountbatten