For both you and Rob...this is a wonderful tour!! Who's your guide? I had Rebecca and enjoyed it thoroughly.
I don't think you can get your Museum Passes early and they are just 2-day passes anyway so you'd need them Wed/Thur. The days have to run after each other so you couldn't use it on Monday and again on Wednesday if that makes sense.
Are you staying at l'Empereur? If so, on your arrival day I would walk over to the Champ de Mars, walk down the garden area to the Eiffel Tower and then back along the Seine. If you want to do a museum you'll be right across the street to Les Invalides and Napoleon's tomb. It is usually open on Mondays and the website indicates it is open April 30.
http://www.musee-armee.fr/en/coming-to-the-museum/opening-times-and-prices.html
On Tuesday, May 1 consider going to Notre Dame - and go inside. The church will be open on May 1. You can also consider going to the Musee Jacquemart-Andre which is open May 1. It is not covered by the Museum Pass anyway.
The Ecole Militaire Metro stop has a manned window so it is easy to buy Metro tickets there if you don't want to try the machine. Be sure to greet the attendant with a Bonjour before you start your transaction, even if you think you are not pronouncing it correctly!
Congrats on your health victory!