Josh,
I’m not personally familiar with the Nordcap kit myself but as far as some general advice is concerned:
1: The deckhouse should fit over a coaming or lip run around the edge of the access hole in the deck, about 1.5cm high should be sufficient to stop water that gets on deck running into the boat. You need to have some way of securing it though otherwise the deckhouse could be thrown off in choppy water. A pin each side passing through the side of the deckhouse and the coaming would be sufficient but there are other ways that may occur to you.
2. A light grease in the prop and rudder tubes will not leak out but will stop appreciable water ingress although you may still get a few drops in up the prop shaft. A tip is to use a close fitting brass washer between the prop and the end of the tube which will tend to seal the end of the tube when the boat is going ahead.
3, 4 & 6 Obviously the planks should be held in position while you are glueing them with tape or similar means. They will need to be glued to each other as well as to the frames and the best glue for this purpose would be aliphatic resin as the excess can be wiped off with a wet cloth and won’t stick to everything else! People do use cyano glues because they are quick drying and you could certainly do this but, as you say, they are not forgiving in this situation and you will need a lot of it which would be far more expensive than using a proper wood glue such as Aliphatic resin. (which might account for the shop’s reccommendation!)
Plank on frame Billings kits are rather notorious for leaking so you will certainly need to seal the hull. Some people advocate just sealing the outside to let the wood “breathe” but most would give the inside a coat of polyester resin at least, ideally with lightweight glass cloth reinforcement which will make the hull very strong.
6. For the external surfaces the wood will take most conventional finishing systems and it is just down to preference. Some people would coat it in polyester resin on the outside too and rub it down before spray painting. My method on a wood hull would be to give it two or three coats of sanding sealer to fill the grain and rub it down to a smooth finish. Then I would use Halfords car body primer spray to give the initial finish. After that you can either use more Halfords colours for the final finish or switch to Humbrol enamels. But if you do use enamel, don’t try to spray over it as you will ruin the finish. Likewise, if you are using spray cans, ALWAYS stick to the same manufacturer as the solvents used by different makes are frequently incompatible.
I’m sure that others on here will add their own pennyworth so read the advice, try not to get confused and ask as many questions you like until you are happy.
Colin