For my first trip to Paris, I started out by printing out the sights listed for Paris Museum Pass. I looked at websites for them and decided which I wanted to see. I then went to Google maps and save each one I wanted to see (click on the star on the left of the page to save). After that I went to TripAdvisor and looked at their top things to do (at least a few pages), and saved the ones that looked interesting on Google maps.
Google maps will show the open hours for each place you click on. Remember hours change for different times of year, but it gives you a good idea which day each place will be closed.
Once I had that, I sorted them into a groups, on the map, so I could have walkable days. I decided which day would work for each group based on opening hours and closures.
I really like the pass because it allows you to stop for 30 minutes at a small museum that might not otherwise be worth paying a seperate admission.
Be realistic about how much you can see in a day. I try to limit museum visits to two hours at a time and focus on a part of the museum rather than spend all day trying to see everything. I also limit how many stops I'll make. Generally, I'd say one big sight in the morning and one in the afternoon is plenty. The nice thing about Paris is you can do that, plus a couple smaller sights that are within walking distance, without feeling overwhelmed and still have evenings to relax in a cafe or stroll.