can you give a bit more information about your boat? Scale, size, ect. Why do the shafts need to come out? Frozen?
Being a surface runner vs a dynamic boat( one with a ballast tank capable of submerging partially or completely) is very similar, only the ballast tank and plumbing is missing. The real issue is water tight integrity for the motors, radio and battery. There are generally two ways to go, a WTC( water tight cylinder, or a pressure hull boat, like the older Engel boats.)
Choosing which route you are going to take will determine where and how you seal the hull.
With all that said, this gets to your shafts. Do they, or did they , have seals on them? or, perhaps the motors had shaft seals?
Anoter wonderful source of information is The SubCommittee.
It can be found here :https://www.subcommittee.com/forum/
Membership is not expensive and the knowledge base is extensive.