How best to get around in this itinerary in France?

A lot of folks like to stay in Paris at the beginning of the trip to get over jet lag, etc. If you did that, you'd end up in Rennes, from where you could drive/train to Nantes and fly to Munich (I think?). You can do MSM as a day trip from Rennes while you still have the car, rather than going out of your way coming from Amboise (and that's a long drive). But it seems like a car is a good choice. E.g., I didn't see a direct train from Chartres to Bourges.

This is doable and not rushed. I agree with spending time in Paris at the start of your trip. Double check the hours that your car rental office is open. In smaller cities, they often have partial hours in Saturdays and are closed Sundays. However you might be able to return a car when an office is closed by leaving the keys in a lock box.

It might be cheaper and much faster taking a plane, rather train to Munich.

Thank you for the replies so far. We very much want to spend the night on the Mont and have it be peaceful at least for a bit without the day trippers.
I already tried this itinerary in AutoEurope and it is not allowing a drop off in Rennes??

Since Rennes is on the way to MSM, depending on your timing, you could just drop the car on Friday in Rennes and jump on the bus to MSM. It runs frequently and is very comfortable (took it from St. Malo with same company).
https://keolis-armor.com/en/5ey-Going-to-Mont-Saint-Michel.html

Try adjusting your return time in Rennes
Since it’s a Saturday agencies likely close around noon

Surprised it allows pick up in Bourges on a Sunday when agencies are closed
( your pick up location might actually be the problem if that agency in Bourges doesn’t allow diff drop off location)

You can call AutoEurope toll free

Auto Europe allowed us to return our rental car at the Rennes airport (Avis), June, 2025. We took a taxi to the train station since we did not want to drive in a larger city.