Nice coop, lucky chickens and chicken owners. And DH is a lucky guy! All that work done and HE didn't have to do it!
Having looked into LGDs, I'm wondering if you and the breeder went over the very serious need to train the dog properly? Especially since you've never had a dog before. I have had dogs (not for ~40 years though and just house pets) and I understand there is a lot more to training a LGD than simple obedience one needs for a house pet. Not only to teach the dog that the chickens are not to be messed with while letting the natural guard instinct develop but also that every person in the house out ranks the dog. I think you will have to train the kids AND the dog, especially if your avatar is a recent picture. The dog will outweigh the kids in 6 months and has to know that he must obey them, not the other way around.
Bee is right on the eggs in the nest thing (no surprise!!). I've only found 1 egg outside EVER and I don't even know when it was laid. It was under an old piece of porch that was taken off the back of the house and put behind the barn. Big boys with big toys are VERY helpful. The excavator picked it up and drove it around behind the barn and placed it over the fence as far as the bucket could reach. I would have had to take it apart and move all the pieces, then put it back together! Of course, I guess I don't know what I don't know as well. They COULD be laying in other places but since I have eggs from all the girls in the nests at some 'reasonable' schedule I'm pretty sure they come back to the coop to lay. I've certainly seen them a goodly distance away and then in the nest later even though all the other girls are still out.
I agree with Bee on the roof. Assuming the rafters are sound, metal roofing is not too expensive and not too hard to install. I found this:
http://roofingintelligence.com/ it might be of some use. Google is my 'go to' resource for repairs
I assume the plywood decking is not in great shape if the shakes are rotting and you can see through in some places. If it is bad, replace it. You don't want to trap a bunch of wet wood under the metal roof.