I agree that the schedule seems a bit aggressive on some days (especially the art museum day), though you can always change it (except for the pre-scheduled activities) once you're there depending on the weather and your moods.
Though some days seem light on activities to me, though I guess that's based on personal opinion. For example, exploring the Latin quarter, for us, wouldn't take too long. We mostly just walk through the Latin quarter on our way to other places.
I've got to say that I would not choose to take a bike tour in Paris, especially at the warmest time of day, with the busiest traffic. We just returned from a trip that included Paris, and saw plenty of these biking groups. I'm glad to see that Paris now has lots of bike lanes, but still, I would be terrified to have my kids riding in them right next to the traffic. Obviously a matter of personal opinion.
For Saturday, I don't know whether your tour includes lunch, but if not, pick up food and drinks for yourselves for a picnic at Versailles (and remember the French have a different perspective than the US, so your lunch can include a bottle of wine).
Your Sunday, I'm not sure what you mean by uphill, I've never noticed an incline, so it can't be huge. This day, also, isn't overbooked, unless I suppose you enter every chain store that is now located on the Champs Elysees. We always spend quite a bit of time watching the cars and trucks and motorcycles and bicycles driving around the Arc; it's death-defying on the part of the bikers, and hilarious to watch.
Whether you're leaving anything critical out depends on your interests. And I think you'll have time to just walk around and stop at plenty of cafes. For some fun and different refreshing drinks, you or your kids could order citron presse, which is a French version of lemonade - they'll bring you a glass with lemon juice, a glass of water, some sugar and ice, and you can mix your own. Also iced coffee can be good, that's cafe glace (with accents, I don't know how to add those).
We've been to Paris a bunch of times, and love museums, but the Paris pass has never priced out for us as a money saver; price it out for yourselves before you purchase, to see whether you will indeed save money. For one thing, kids under 18 are free into museums. Just go to the museum (and other attraction) website and buy tickets online in advance. You'll still have to go through security lines, but not lines to purchase tickets.