First, let me say there is no substitute for a good map. If you can find your "must-see list" on the map, they will almost group themselves.
Second, if you are a Monet fan, you probably should include the Orangerie and/or the Musee Marmottan. The Marmottan is not on the museum pass.
You can walk from the Louvre, through the Tuileries (a lovely park) to the Orangerie. Both the Louvre and the d'Orsay get crowded, so you might want to do them separate days and get there at opening. Make sure you already have the museum pass in hand to avoid the line to purchase.
The Saint-Chappelle and the Concierge are virtually next door, so if you intend to do both, it makes sense to do them in sequence. Notre Dame is an active church so you can go in anytime, but the pass allows you to do the tower climb, which was a highlight for me.
The Eiffel Tower is not on the museum pass, IIRC.
A lot of experienced travelers don't care for him, but for a novice like us, I found Rick Steeve's website to have very useful information. He gives sample itineraries of one to seven days in Paris, to which you can use as a starting point and add or subtract as you see fit.
http://www.ricksteves.com/plan/desti...rance_menu.htm