Timing advice needed for visiting Orsay and Marmotten

It might help to get a map and pin each of the places you want to visit, to see if you can logically group them. Then see if any of your walks could fit between any of them. We usually try to block plan, with one "must see" each morning and afternoon, and sometimes one in the evening. Any free time in between can be used for a second tier site or activity. I'd definitely do the Seine cruise in the evening, just after sunset. I hope Monday isn't your arrival day. I noticed you have nothing planned that morning. Your list is long and your time is short. I fear some pruning may be needed.

I just looked up the concert as it sounded like something we might want to do during our time in Paris (Aug 28/29 & Sept 6pm-Sat10am.

Unfortunately, the concert does not appear available on Sept 6, 7 & 8, so you would only be able to catch a concert on Monday ---I wish we would be there a day early as that day incudes Vivaldi's Four Seasons.

Orsay is open late on Thursdays, until 945 pm. Why don't you fit it in then?

If you can't fit in Rodin Museum, maybe try to see the gardens at least? They're lovely, and 30 minutes will do!
Otherwise, after Arc de Triomphe, I'd go to Marmottan. It makes more sense geographically speaking, and it is a much smaller museum.
Likewise, Orsay is adjacent to the Latin Quarter (or rather to Saint Germain des Prés) so it makes a lot of sense to combine them!

I actually found the grounds of the Rodin museum more interesting than the exhibits inside. Out in the air there are just sculptures, inside there are drawings and plans and renderings and tests and and and. Even Rick admits it gets a bit tedious after a while, so if the weather is good I say stay outside. Unless there's a special exhibit on offer as there was during our visit.

It’s best to get to Paris’ top sights ( the Louvre, Musee d’Orsay and Versailles Palace ) first thing when they open. After that, the lines grow longer and you’ll find yourself standing in them instead of enjoying the attractions. Even with the timed reservation slots these museum’s lines back up and delay entry times. I found the Musee d’Orsay gets crowded mid-morning. so I would plan on it for right at opening time ( 9:30am) if you can’t do an evening visit. The Rodin museum is 1/2 mile away so it works well then. And, yes, the statuary in the outside gardens are more impressive than the contents inside the building.
I would prioritize those sights for the first morning slots and do the Montmarte and Latin Quarter walks in the early afternoon.
The Musee Marmotten is by itself, west from the Eiffel Tower. It’s 2 miles from the Arc de Triomphe so it isn’t all that near anything else on your itinerary so probably should plan on taking the metro to get to it at a time that works.
St Chapelle’s concerts are generally in the evening. But be sure to see St Chapelle during the daytime when all those ancient stained glass windows flood the chapel with color. You can’t see that at night. St. Chapelle is near Notre Dame Cathedral if you were going to be viewing it from the outside.
Have a great Trip!