Ok, good to know your thoughts!
First - the Museum Pass covers consecutive days only, so you'd need to bunch your Museum Pass sights over maybe 4 days.
The sites where the Paris Museum Pass can be used that are currently on your itinerary are:
Pompidou
the Orsay
Louvre
Pantheon
Arc de Triomphe
Versailles
Napoleon's Tomb/Les Invalides/Musee de l'Armee
Here are my thoughts:
Thursday: Looks fine
Friday: To me your Friday is WAY too much. I'd never be able to do 3 major museums in one day. I'd suggest you move the Orsay to another day. They are closed on Monday.
Saturday: You could move the Orsay to this day. Go to the Luxembourg Gardens for lunch, perhaps. I like La Terrasse du Madame if the weather is nice as they have a wonderful outdoor area. Put the Pantheon after the gardens as they are literally 3 blocks down a main street and you can see the front of the Pantheon from there. Are you Midnight in Paris fans? I'm not a big Woody Allen or Owen Wilson fan but I love this movie! The time-traveling taxi picks Gil up from the steps of the Saint-Etienne-du-Mont which is just off to the left behind the Pantheon. There is also a very cool double helix rood screen in the church as well as a reliquary of Saint-Genevieve, the patron saint of Paris.
Sunday: Maybe you could move Versailles to today? Although SUnday can be really busy if it's a day the fountains are turned on. The things you have slated for today will work together any day. TBH, I'd wait until the last minute to decide on Pere Lachaise as it works better if it's a sunny day. Be sure to download Rick's audio app on your phones and have your ear buds with you.
Monday: Your Monday activities can also be moved around as none of them have closure days. You could move your Eiffel Tower and Napoleon's Tomb day to today as they are open every day.
Tuesday: Your grouped sights for Sat, Sun, Monday or Tuesday can work today as none currently are closed on Tuesdays.
Wed: Again, any of the combos can work today.
Thursday: You'll have so much today that you still want to see, lol!! Maybe a Paris Walks tour today? Or a food tour?
So...I would reconfigure things if you decide the Museum Pass will work for you after adding up the admission prices of the places you want to see. I'd bunch your Museum Pass sights over Fri/Sat/Sun/Mon. While many museums are closed on Mondays, the main one you want to see that has a Monday closure is the Orsay.
Wow, I'm pretty bossy this morning, lolol...AND I've not even had coffee yet!