As far as 700 cc. wheels, we use Mavic rims often and I suggest a spoke count of 32 with the cross 3 pattern, granted if you aren't planning to be loaded you could go down to 28 but this way you would be prepared for the future. I also tour with a dynamo hub because I love having a light and never having to worry about being caught somewhere after dark.
Tires - 700 X 28 - no narrower, Will be a way more comfortable ride than using a narrower tire and you aren't going to notice rolling resistance - regardless this is a tour not a bike race . We love the Schwalbe marathon - supreme or dureme should be sturdy enough, we also ride Panaracer TServ's - the Bike Hermit has ridden 1,000's of miles on those.
Brakes - without a load, I consider disc brakes an overkill. Fenders will work with Disc Brakes but it may take some finesse to attach correctly.
Fenders - but of course, SKS long boards are sharp and disc brake compatible, Tanaka and Honjo's are great too. Planet Bike Cascadia touring is another option. All based on what you want to spend and ease of install and removing.

Sounds like a terrific goal and a fantastic adventure! Oh and the co-motion is beautiful. I happen to have a 52 cm Rivendell Sam Hillborne in my garage that is a tad to long in the top tube for me if you were so inclined but I am also considering changing out the handlebars from drops to more upright position and making it my "adventure touring bike" I love my Bleriot and ride her all the time.