Hi Johnny and welcome to the forum. As usual with such questions there will be as many answers as there are members but I think we will all be in the same ball park.
Your model is fairly small and not performance based so I would go for something along the lines of a 360 to 385 motor. I would have a chat with these guys to get an exact recommendation.
Como Drills
This is a more expensive route than picking up something off Ebay but you know you are getting quality and a good support service.
Once you have your motor identified you should then have a good idea of the current it will draw so you can then select your speed controller. There are lots of Chinese speed controllers available on line and through various outlets but, for myself, I prefer to use a British based manufacturer who are always available to help so, for me, this would be Mtroniks:
Mtroniks
I would go for a waterproof Viper speed controller, which are designed for Marine use. I would guess you would be going for a Viper marine 15 or 25. This also includes a power supply for the receiver so you are saving the weight of another battery for that, and a power switch to switch everything on and off.
The battery is very much dependent on your ballasting situation and how much capacity you have available as regards weight. For such a model though I would expect that a 7.2 V NimH pack would do the job and a capacity of 3000 or 5000 mah would keep you going for a couple of hours. This would also sit nice and flat in the main hold so keeping your centre of gravity low. This is a typical battery, again from a UK supplier so you have a degree of support and a better quality product:
Component Shop
Finally don't forget the radio requirements and always include a suitable sized fuse in the positive lead from the battery. This should be rated less than the amperage of the speed controller.
As regards the shaft there are a couple of possible suppliers such as Cornwall Model boats:
Cornwall Model Boats
Those with plastic bushes tend to leak a little bit more but putting oil in them can help and, of course they are cheap. With your type of model the inner end of the shaft will be below the water line so will tend to leak that little bit more. The best shafts are those fitted with sealed ball bearings at either end, which are obviously more expensive but seal better. For your model I would prefer a ball bearing type. I have a 1/32nd scale raised quarterdeck coaster and fitted a ball raced shaft tube in it for that reason. They do require slightly more power to turn but this will not be an issue for a low performance model.
Let us know how you get on.