Wed: I'm with CL...I would absolutely go to sleep on a bus ride on my arrival day BUT you may be different. Your profile looks like you're from Edmonton so you probably have as long as flight day as CL does from Portland and I do from the Inland Northwest. As long as you don't have to purchase this ahead and can go on how you are feeling, then leave it in the plan. What time does your flight land? You might be able to walk the Latin Quarter this afternoon OR if it's a pretty day even get to either Luxembourg Gardens or Tuileries. IF it's rainy, maybe some of the passages.
Thurs: I would not use the Batobus for transportation. You are doing a cruise so this will be redundant. I'd just take the Metro to Ecole Militaire on LIne 8. See the ET, come back for lunch in the Rue Cler area. I'd not try to do the Invalides AND Orsay on the same day. The Invalides is huge unless you are just going to pop in to see Napoleon's tomb. I like the WWII galleries here and the Legion of Honor Museum but that will take several hours. You could do Rodin afterward especially if you just do the very cool sculpture garden. IF you decide Orsay is a priority, I'd get there when they open at 930, so that, walk to Rue Cler (takes me less than 25 minutes) for lunch, do the Eiffel Tower, then see if you feel like either Invalides or Rodin.
Friday: This looks like a lot but you can just dip into the edge of the Latin Quarter across from Notre Dame unless you walked over there on your arrival day. IF it's rainy, you could probably do the passages after Notre Dame and before the Louvre as they are nearby. To me, 1 or 2 is enough to get the cuteness factor.
Saturday: To me this day is overloaded if you do a food tour AND a tour of the Opera Garnier.
Have a wonderful time!