1) Nests: I know that Muscovy prefer nest boxes on the ground and that the moms remain there steadfastly, so I need to choose a good location. I was thinking that I would just build them and lean or attach them to the coop since the feed is in there, so everyone is fairly close together. Is this a bad/good idea? Should they be further away from the main coop or further away from each other?
It depends, really. Sometimes there will be fighting over or sharing nests & that in and of itself can ruin a hatch. You can see examples of how I set my nest boxes up
HERE. I make sure that they're in the shade & on the ground & that the back two openings are partially covered so that the duck feels secure. It is worth noting that we do not get a lot of rain as a general rule & have been in a drought for 7-8 years. You might have to make modifications if you have especially wet/muddy soil regularly.
2) When should I plan to have the nests out and ready? Do I need to time it, or just put them out whenever and the moms will take up residence when they're ready?
My friend has his birds in breed pens in January, I don't put mine in until March or early April. Nest boxes are in breed pens as soon as the birds are put in. The longer your winter the more time you have in the spring.
3) I've lost a couple over the months to raccoons. So, I'm planning using electric netting around their area to try to protect them a bit more. Will that do, or do I need to close up the nests once their sitting and provide individual feed and water to protect mom and eggs during hatching time?
You don't want to put feed or water close to the nests at all. You want the bird to get off the nest once a day, get some exercise, go for a drink, a bite to eat, a poop, & then they will preen before getting back on the nest. Don't want any of this near the nest. I've actually warned a guy against putting food/water next to the nest and within a matter of days that nest was annihilated by a predator. He believed me after that!
As for the electric netting, if the birds will stay inside it they'll be fine. They might fly over in their search for nesting sites. A well prepared, secure feeling nest box is one way to encourage birds to lay where you want them as opposed to where they want to be.
4) I'm in northern WV so it's still cold here and spring is still a few months away. When should I anticipate them starting their first clutches? Then the next ones?
I'm not familiar with your weather so I can't give you a better date as to when they'll begin to lay, you'll just have to watch their behavior. As for subsequent clutches, birds who raise ducklings won't lay until the ducklings are 6-8 weeks, generally. Sometimes more, sometimes less. If you take the ducklings from the duck they'll begin laying again in 2-3 weeks. I tend to do a fostering system where I put multiple clutches together and re-introduce the duck with the oldest clutch back into the breed pen (if I'm wanting more ducklings!) and allow the other hens to mother her babies. Works well if the ducklings are similar sizes. Too big of a size difference can result in aggression & picking by the older juveniles.
5) I feed waterfowl pellets and the occasional treat, and they forage of course. Should I supplement the mommas with something extra before, during, or after or is the free choice pellets all they need?
Oyster shell would be a good idea. I like to give my birds an animal protein in their diet which is actually in the poultry concentrate I use. Muscovy are especially omnivorous & benefit from it. It can be cat food, fish meal, etc.
6) Are there any good "duck" books that anyone can recommend specifically for Muscovy care, breeding, and health?
Storey's Guide is about the best one that I'm aware of. It has the most information as far as I know.