That's a rather complicated question that would take a long time to fully explain, but I'll do my best:
First, you could check out this link (especially Seven Characteristics of a Good Coop):
http://www.raising-ducks.com/accomodation/housing-basics/
It doesn't have very much information yet, though. It is my own website, so I will try to hurry and write more about housing for you! You could also search on BYC to get more ideas.
Secondly, since you live where it is cold, it
might be necessary to insulate. Generally, this is not needed, but Muscovies are tropical ducks and can get frostbite in below-freezing areas. You will also need something so their water doesn't freeze.
Yes, the nesting boxes should be on the ground, and dirt is the best bottom for the nests, but dirt may not work if it freezes where you live. I've had some Muscovies that REFUSED to lay in a nest with a wire, wood, or any other floor than dirt with hay on top! As for how many nest boxes, you need about three.
I'm not sure what you mean as far as which type of ventilation, but you need as much ventilation as you can get without getting drafts and lots of wind. I've read that the way you can know if you have too little ventilation is by how much condensation there is on the roof. The ventilation is ideal when there is no condensation and no direct drafts/wind.
Also, make sure it's predator-proof. If there is a dirt floor, there may be predators that try to dig under the walls. This is usually fixed by extending the wall underground (though I'm not sure how far you should go).
It has to be easy to clean. If it's too low, it will be hard for you to get in to clean it. You need to have some sort of bedding so you can clean it, since you can't clean the dirt. Personally, I think either straw or sand is the best, but there are other options.
I hope this is what you need!
~Hannah