Schedule Second Time in Paris

I'm not sure what kind of suggestions you're looking for. Do you think your itinerary is too busy? Are you wondering how to figure out the Metro or bus system?

Pere Lachaise cemetery is free, but they want you to buy a map so you can find gravesites of interest. There are no signs for graves within the cemetery. My sister and I thought this was a bit of a racket. We didn't buy a map and instead asked cemetery employees where to find graves. We also started at the bottom of the hill and worked our way up, which was kind of a hike.

Since you're visiting Versailles, the Louvre, and the Musee d'Orsay, you might consider the 6-day Paris Museum Pass. You have to use it on 6 consecutive days so if you want to buy it, you'd have to rearrange your museum-visiting schedule but it might be worth it. Add up admission to each place and compare the total with the cost of the pass. The pass also allows you to skip long ticket lines at the 3 places I mentioned above. I'm not sure if the pass covers Napoleon's Tomb or the Military Museum.

Be aware that there is an extra charge to visit Versailles on days when the fountains run. The Museum Pass doesn't cover this extra charge.

Museum pass DOES include Military Museum (Napoleon's Tomb) so you could use it for 5 days within a 6-day period.

That's plenty of great destinations. Aside from planning around closed days or late openings, as you have done, I think you can let yourself be flexible, in case of rain, tired feet, street markets, or other attractions that pop up. The Museum Pass helps with flexibility, letting you pop in for a short visit without feeling like you paid a big entrance fee.

It all sounds wonderful to me.

I'd also recommend the Museum Pass. It saves you standing in ticket lines (but you still have to go through security), will probably save you money overall, and also makes it easy and "free" to pop into other museums that you may encounter, maybe just to see one or two things.

I think your plan is well paced, though I just can't relate to four whole days at two flea markets! ;) La Defense is impressive but won't take long, you might find yourselves having brunch or lunch at Laduree before tacking the Louvre (which, as you know, can easily fill the rest of your day and evening). St-Denis is a good choice that most visitors miss. Pere Lachaise is best approached from the uphill side, take the Metro to Stalingrad and work your way down through the cemetery. Near the Invalides is the Rodin sculpture garden, a pleasant retreat in good weather for a one-euro investment.

I think you'll find you have time for more spontaneous improvising (made easier by the Museum Pass). Just walking around this beautiful city, with café stops for coffee, wine, and bathrooms, is enough for many hours of enjoyment. You should have good weather in May.