My unwanted comment: So sad you going with pre conceived shots! It is a tremendous city and if you let yourself go you may just get unique great photos. My two cents.
Think of it more as a scavenger hunt with the applied science of technique.
Quote honestly, if I didn't have children in tow, I would be more adventurous... But I have one child who is pretty and the other who is possessed by the devil... So I spend a good deal of time making sure they stay alive.
That's why I am going with a checklist... So I can get something done... in lieu of just photos of my children and wife shopping... because that is what I'm most concerned about.
My best advice, as someone with a family, keep it simple on the shots and the gear. Like it or not, the family is the focus. (It sounds like you already understand this but I had to say it anyway to make my point.) You'll quickly get irritated that your enjoyment of the photography is lacking due to the family or vice versa.
Why do you need the 600EX flash? Get a small low profile SunPak RD2000 or Canon 270EX-II (with Sto-Fen diffuser to match) to use for fill and leave the monster flash at home. Most of your shots of the city or architecture won't use flash anyway.
When I am on trips like this, I usually take the same gear I take on many other outdoor ventures... 5D3, SunPak RD2000 flash, 24-70 or (not and
) 24-105 as a primary lens, 16-35 wide lens and 15mm FishEye. Other than a shoulder strap and small lens bag that holds both off camera lenses together + a little padded zipper pouch with extra batteries, media, etc that's it. I put the lens case in a basic no frills daypack and depending on the destination, I might also throw in a CPL. Sometimes I carry a small S120 P&S camera or a D20 Rugged P&S to hand to others to use or in case I need to be more discrete and put away the DSLR completely.
I'm also not sure why you want to drag a heavy expensive prime like the 85L-II around since it's primarily for single portraits but it's your gig. I would think you could achieve something 'good enough' with the 24-70 f/2.8L. Or even the 24-105L depending on the subject distance from background. No offense, we all have our own styles and desires, but I keep the walking kit as simple as possible. The FishEye lens is my 'luxury lens' because it is small, light and very versatile in some situations, esp with lots of people in a group which is common for me in our scout troop. Maybe you could substitute a EF 50 f/1.4 for the 80L to save space and weight and still get the desired shots?
The other stuff that is a good idea would be a rain jacket and/or umbrella that fits easily in the daypack, water bottle (disposable for city security) no pocket knife (because you might take over a building or the subway or hold the city hostage or something with it), and a handy Metro Card or work the Day Pass thing (ugh).
Again, it sounds like you are pretty astute on this but I try to implore everyone I give advice to in these situations to keep it simple and go as light as possible. It's a little easier to go light in the city since you can buy most of what you need in terms of food and drink.
Have FUN!! Enjoy your trip and please post a few pics of you and your family!