Paris is my favorite city so I have lots of ideas.
The first thing that struck me is that you will be there in September. September is a huge month for trade fairs so expect most hotels to be fully booked well in advance. This doesn't impact tourist sites much, they aren't any more crowded that usual. The other thing about September is the Journees de Patrimoine (heritage days) which are usually the 3rd weekend in Paris (most European countries celebrate, but some at different times). You can choose to avoid Paris then or take advantage of these special days. Besides the usual (e.g., most museums are free) the government opens buildings to the general public that are usually restricted to those with authorization: the ones I saw were the National Assembly, the Senat (aka the Luxembourg Palace) and the Hotel de Ville - these were all palaces and they are beautiful. The longest I waited in line was an hour, once inside you are free to take your time (and your photos) for as long as you like. Most other governments offices were open as well as some of the embassies (also in palaces, of course). I visited the Russian Embassy which had a special exhibition on the Romanovs (and lots of Faberge) for the event.
The main advantage to the museum pass for me is that I don't feel I have to spend a lot of time in a sight to justify the entrance price or skip a sight because it may not be worth the money.
I start with a spreadsheet of all the sights that sound good to me. The museum pass website is a good start to build the list. I list the hours (especially any evening hours), if they're included in the pass, and the arrondissement (its the last 2 digits of the zip code). For some places it saves waiting in line - another bonus.
I always walk my legs off in Paris, so I ride the bus or metro as much as possible. The most economical and convenient option is the Navigo pass, which is weekly from Monday-Sunday. If you get 5 consecutive days it's usually money-saving, at 3-4 days you are around break-even, depending on how much you'll use it. It's good for both buses and metro. You need one per person and there's an initial fee of €5 each, but the pass is then good forever. So if you can be flexible with your days in Paris, plan to arrive early in the week for maximum savings on local transport.
One of my favorite museums is the Carnavalet in the Marais Quarter. Please don't skip it. It's the history of Paris, very interesting, beautiful building. Probably the reason it isn't included in the museum pass is because it's free.
To avoid crowds as much as possible:
Louvre enter through the Carousel, not the Pyramid, entrance. Visit from late afternoon on one of the late nights, Wednesday and Friday. If you want to rent an audio guide, remember which kiosk you get it from, so you can get your driver's license back when you return it.
Orsay I think the museum is too small for the collections. It always seems crowded. My best advice is to get there when they open and start at the top. It's where most of the "best stuff" is and most people work there up so it will be relatively empty.
Sainte Chapelle The security line can be really long, because it is also the entrance to the law courts. Also when I was last there, they were closing the entrance for about an hour at lunch time! The best way to see this is to get tickets for a concert. It's usually light classical - Vivaldi's Four Seasons is a standard. There are often two concerts an evening, get the one around sunset - the best time to be see the stained glass. Be among the first to arrive and you'll have lots of time to get good seats, then wander around looking at the windows (and taking photos) before the concert begins. You don't get to see the lower part of the chapel, but the upper part is what everyone goes to see anyway.