Please help refine our Antwerp/Bruges/Brussels itinerary?

Sure, that works fine. Can't speak to the museums in Brussels, been there 4-5 times and have not hit those, just different interests. But Really, Brussels is what you make of it, I did it the first trip in an afternoon, and was fine, the trips since, passing through or staying, have been focused on beer. I enjoyed Antwerp more than I could have imagined, it has a nice vibe, interesting city center, feels more like a nice city than Brussels (Brussels can be a bit crowded, overtly touristy, dirty). Bruges is Bruges, quaint, touristy, but in a nice way. Ghent you might feel like you short-changed yourself, great old town, good vibrancy, more of a local feel than Bruges.

Do you know what you are going to do in Ghent? Do you want to subtract a night from Bruges and add it to Ghent? Or do you want to delete Ghent and add a day to Antwerp? Antwerp deserves an extra night if you like museums. Otherwise 2 night there will be ok. On my one full day I gave myself in Brussels, I only gave myself time for the art museum and the Manneken Pis statue. For your day 6, you might want to rank the 4 places you listed in order of importance, don't rush too much, and assume there is a 25 to 50% or more chance you won't make it to the last one or 2 museums. The Margritte museum is one of 3 parts of the art museum. When I was there in july 2019 I had the option of paying for just one or 2 or all 3 of the 3 sections. I skipped the Margritte museum. I wish I had seen it. The whole museum has enough to occupy yourself for the whole time of the day they are open or more if you tried looking at everything. Pick up a museum map when you arrive and pick which sections to see first, don't rush and assume there is a big chance you will acquiesce to skipping some sections. You might have to buy advance tickets for the European Parliament. I didn't make time for it. I have no clue what I missed.

I skipped Bruges. I would have been happy to go there if I had planned my trip differently. I took a day trip to Ghent. When you get off the train in Ghent, you can get on a light rail commuter train and get off by the Gravensteen castle. Then there is a big patio with tables with umbrellas over them across thentracks from the castle. If you cross the patio and go through modern glass doors at the inside corner of the L shape where two buildings meet, you will be in the tourist office where you can sign up for a walking tour. Mine started at 2pm. I thought the castle was worth it. I didn't feel like it was kid-oriented. It is good for ages 7 or 8 through adult. (Rick says to get off the trolly somewhere else before the castle. Rick was wrong.)

I'm going next month and can suggest a few things from my notes that I don't see you mention. Depends on your interests, of course.

Antwerp: Cathedral of Our Lady, Saint Charles Borromeo Church, Sint-Jacob Antwerpen.

Bruges: Sint-Janshospitaal, Church of Our Lady, Basilica of Holy Blood, Sint-Salvatorskathedraal, Groening museum, Belfry.

In Antwerp you can visit Zurenborg, an urban quarter with lovely turn of the century (19th to 20th) architecture. From Grote Markt you can walk to it via Groenplaats, Wappert (along Rubenshuis), Stadspark and Mercatorstraat / Cuperusstraat along the railway track to Antwerpen Centraal. Taking a tram is possible too. Further a walk through the Diamond Quarter next to Antwerpen Centraal railway station, the architecture is not so much interesting but knowing this is still the world’s main diamond trading hub it has something special.

In Bruges you can walk to the windmills at the north-eastside of the historic centre via the Jeruzalem Church, Carmenstraat or Rolweg. Along the canal to Damme you can bike further to Oostkerke and Sluis just across the border in the Netherlands. The latter very touristy but has like Damme ramparts with a footpath offering views over the place. Detour to Sint Anna ter Muiden is worth the extra few km.

https://community.ricksteves.com/travel-forum/belgium/day-trips-from-brussels-768c7c85-75b9-4374-ad13-ae36967bc521

There is considerably more to do in Antwerp or Brussels than there is in Bruges. So I'd move one Bruges night to Antwerp. But I know that many posters here think Bruges is the most beautiful and romantic place on earth. I don't, I just think it's a nice, historic, visit. And I don't care how much "better" it is before the tour busses come. You didn't mention the religious art museums or the Michelangelo sculpture in Bruges, or the famous UNESCO WHS Beguinage.

The main art museum in Brussels is quite famous, and can't be seen fully in a day! (Royal Art Museums.) Unless your family is big on immigration, I would put the MAS museum or the Meyer van den Bergh museum way ahead of Red Star. The Rubens HOME is not a museum and has a microscopic collection of actual ARTworks. That said, it's a nice classic mansion. Most of the Rubens paintings you may find on show in Antwerp until September, 2022 are on loan from the KMSKA museum which is closed until renovations end. I don't know which museum has the most right now, but MAS would probably have some. Reubenshuis does not have enough security or air conditioning to show important Rubens oil paintings. The Rocoxhuis mansion-museum actually owns some Rubens works, and is a nice, less-crowded visit.

We spent 3 nights in Brugges. On one day we took Quasimodo’s Flanders Field tour. We also took a canal ride. We spent 2 nights in Antwerp. Two unique sights we visited were a 1930s era all wooden escalator by Sint Anna’s tunnel and Het Bootje. It is an art Nouveau building with a ships bow sticking out of it. It’s at Plaatsnijdersstraat 1 and the corner of Schildersstraat. In Ghent, two places many tourists don’t walk past are Glass Alley/the small red light district by Pieter Vanderdoncktdoorgang 1 and Werregarenstraat. It’s an alley with bright paintings/graffiti. Everything else we saw were the typical sights.

We’re not all that keen on Brussels. Other than the Grand Place we don’t find it interesting. A couple good chocolate brands are Mary (chocolatier to the royal family) Neuhaus, and Galler. Everybody stops by to see The Manneken Pis statue. There’s also a Jeanneke Pis statue. It’s a little harder to find.

Thank you, everyone, for all of your replies! I will rework our itinerary to include your ideas! I'm sure we won't get to everything but you've given me a great blueprint.

Please report back and let us know all about it :-)