12000 rpm from 4.8v is pretty serious, and also explains why you have trouble throttling the motor… the very low volt range and a wickedly powerful motor. A motor with a larger voltage battery can be throttled with a bit more finess.
Still. like me, do what you are happy with, and after all, that sort of speed and 90 mins duration cant be all that bad!!
I have no trouble with balsa as far as waterproofing goes because as it soaks up water, so it soaks up a sealer, such as a cellulose sanding sealer. In the raw unpainted state, splosh the stuff on liberally and then give it a good sand, then paint. The beauty of cellulose sealer is that it will stand a bit of can spraying, which makes ships such as yours (all grey) so much easier to paint.
I always think that the freeing ports are a bit double edged sword on a model..the weight of water is not so much of an issue on a model, compared to the real thing, but its just as likely to let the water on deck in the first place as to drain it off, considering the non-scale waves.
You do need some holes of course, otherwise it would look a bit silly with all that water on deck! Stopping the water entering the hull via the removeable superstructure has always been my no1 aim, as this allows you to partake in some serious rough weather boating that leaves others in dock (the car).
Your model does appear to quite stable on the turns etc, but a pair of fixed fin stabilisers, or something similar really does damp down oscillations when weaving or being hit by sudden wind or duck-waves.
Ashley