Thanks for the generous number of suggestions. To explain a little bit more to any of you that are now interested...
The submarine is a 'wet' submarine, with a completely encapsulating hull. The pilot will breathe off a scuba system which is integrated into the sub. Because there will be water inside the submarine hull at all times, the entire drive system will be in contact with water. This includes the crank, spindle and bb, as well as the cogs and chains. Last year we ran into problems with our chain slipping on the cog teeth at depth due to the fact that the chain was not tight enough (we used wood for supports and it deflected under load). We are looking into eliminating the chains all together. Since we are developing a more structurally sound drive frame this year (aluminum), we should not experience issues with chain tension, if we do choose to use them.
From your suggestions, I feel that the more feasible solution might be to machine our own bottom bracket, with appropriate threading which can be welded onto the frame plates. We can purchase a spindle (103mm are the shortest suggested) to insert. We already have 5.5'' cranks which have little bend in them which we should be able to use.
If anyone else would like to offer additional suggestions on the solution (or corrections), feel free.