Sounds like a great trip! I agree about the Museum Passes - the freedom to bypass long lines and pop in and stay a short time was great for our family, and we got to see a few cool sights we might not have chosen if we had to pay admission each time. It also gives you easier access to interesting, cool (temperature) places and bathrooms if you are away from your hotel for hours on a hot day, as we were last summer.
Nighttime hours were a blessing for us during the heat wave we experienced - and we, too, had some galleries in the Louvre all to ourselves as we explored in the evening. That was really an unexpected bonus in comparison to the masses we'd experienced earlier that same day. We went to the Orsay on that museum's late night, too, and really enjoyed it. It was light for so long that we could stay until closing, and come out to twilight in Paris - and cooler temperatures. :0)
If you do go to the Orsay, I'd suggest heading first for the cutaway model of the Opera Garner on the ground level - very interesting for our kids. Then head right up to the 5th floor for the overview of the museum and talk with your kids about how the building used to be a grand train station. Then enjoy the Impressionist galleries.
On that level, you can walk right up to one of the clock faces and look out over Paris. One of my favorite pictures we took was a silhouette of our daughter looking out at Paris through that clock face. You can see Sacre Coeur from that view - and maybe that's enough of Montmartre for your family on this busy trip?
On your way out, you can pick and choose which other galleries you want to dip into, and see the sculptures as well. For me, my top priority at Musee d'Orsay is the Impressionist gallery - so that is how I've planned my visits (several over the years)
There is a Marks and Spencer store near the Luxembourg Gardens, where you'll find a lot of delicious food choices for picnics. When we returned to Paris after a weekend with friends, we couldn't check in to our hotel yet, so we left our bags there and went in search of lunch. We all found great food and drinks at Marks and Spencer. It was an interesting experience to see the international foods available! We then walked over to the Luxembourg Gardens. There are chairs everywhere - sun and shade - and it was a relaxing way to have an inexpensive and casual picnic for five. That store had a deal in the summer that if you spent 20 euro, you could choose a cooler or picnic blanket for free. We took advantage of that, and our picnic blanket traveled through Paris and then to Switzerland with us! If you think that sounds like something your kids would like, ask your flight attendant if you can keep the lightweight blankets from your flight - ours encouraged us to take them for picnicking! That was a surprise. :-)
We saw kids riding ponies, and happily pushing sailboats at Luxembourg Gardens, and also saw a place in the Tuileries where kids were sailing boats. There's a Ferris Wheel in the Tuileries - I wish we'd done that at twilight for the views we would have had. There are carousels around the city - beautiful works of art that looked like fun.
Seine Cruise thought - when we did this with our jet-lagged kids, we made the mistake of sitting in the more enclosed area. Either we were really near a malfunctioning toilet, or else the water itself had a bad smell - but it was an overpoweringly unpleasant smell. I'd recommend being out in the open air for this cruise with your kids.
Our kids had day bags that would hold a small water bottle, things they wanted to have with them, and snacks like Luna Bars and granola bars. We did bring some of those from home, because they were portable, and we needed to have some quick protein snacks on hand. We tended to refill water bottles in museums on those hot days - so I'd recommend that. They also had fun using their phones to snap pictures on their own.
Enjoy your trip!
Laurie