Stacy,
Lucky you! Janettravels44 suggestion to stay in places in chunks of one week is a good one, or 5 days at least. And acraven's idea to lease a car, since you will be there for so long, is another good suggestion. Back in the day (1974!) when we were in our early thirties, we went to Europe for four months. (Lucky us!) We did it on the cheap, with the occasional night spent in the VW Beetle we picked up in Germany. We rarely spent just 1 or 2 nights in a place, unless it was a stop between 2 locations.
Read up on driving hints on this forum, for each country. We loved the freedom our car gave us and found lodging when we arrived in a town or city (often recommended in Frommer's "Europe on Five and Ten Dollars a Day"). Alas, those days are long gone, and I highly recommnend securing your lodging ahead of time. And look for places with available parking. Don't get your car until you leave Paris, and return it before staying there again, if that applies.
Gites de France is a wonderful site to find lodging. We have found places for one night up to 10 days. Just rooms, such as a bed and breakfast, are called chambres d'hote. We have done those, as well as renting a large house for 10 days. Booking.com is good for finding lodging to fit your needs. I found places there and then booked with the hotels, etc. directly. Sometimes I used Booking.com, and sometimes I booked with Gites de France. Put in your filters to save time in searching.
Re itinerary, I know France best, so of course I recommend my favorite places...Brittany, the Dordogne/Lot area, and Provence (and always, Paris!) Look through Rick's or Frommer's books on France to get inspiration and ideas. Perhaps a counter-clockwise trip:
Paris, through Giverny and Rouen to Bayeux, Mont St Michel, and Brittany (2 weeks easily). Next the Loire (3 days) and/or the Dordogne (a week). Then Provence for a week, based in Arles or St. Remy de Provence. Parse out four weeks for France. With four weeks left, I would head to Austria and Germany via Switzerland. As beautiful as it is, I am not as enamored of Switzerland as others are. I don't ski or hike, so just admiring the mountains on my way through is enough for me.
From Switzerland go to Vienna, an underrated city. In 1974 we would sit on the grass in Vogelspark and listen to the band concert there and watch the couples waltz. (If you sat at a table you had to buy a drink.) Vienna has a wonderful art museum with lots of Bruegels (one of my favorites), Schonnbrun Palace, Grinzing, the opera house, Lippizaner horses to see, the lovely ringstrasse, and the best cafe ambience! We spent 5 days there.
Then off to Munich for at least five days. It is a city of fun and exuberance, in my opinion, underestimated by many. From there follow the Romantic Road to Rothenburg and points north, ending in Alsace. By this time you may have 4-7 days left to see Colmar and /or Strassburg and the villages in the wine country there. You can return your leased car where you picked it up, somewhere outside of Paris. A paper Michelin map of France and Germany will show you the big picture better than on online map. I find them indispensible in routing our trips. (Amazon has them, between $13.00 and $20.00, a good investment and souvenir of your trip.) The website viamichelin is helpful for routing from place to place, offering options for your route (e.g. fastest, most scenic, toll costs, etc.)
Dive into this forum when you have a better idea of your route, drilling down on the places that interest you.
What fun you have in store!
Bonne chance et bon voyage! Amusez-vous bien!