Paris and Germay

Seeing that you're willing to drive is good since Bavaria is best seen with a car. I'd suggest the 6 nights in Paris followed by 7 nights exploring Germany and Austria with a car and then the final 3 in Munich.
After Paris take a train to Trier, rent a car there and then spend a night on the Mosel. Continue to the Rhine, then to Rothenburg, down the Romantik Road to the Royal Castles, then on to Salzburg and Hallstatt. Driving will give you lots of flexibility and enable you to see many places you can't get to on a train. You'll save some $$ and problems if you both pickup and return the car in Germany.

I agree with Tim's suggestions. Having a car in Germany is a good idea. So much of Bavaria's special charm is in its winding roads and pretty villages. If you are ending by driving to Munich, why not spend the night before in Reutte, Austria, visit the castles in the morning then drive to Munich in the afternoon. There are a number of great places to visit between the castles and Munich (Oberammergau, Wieskirche, Ettal Monastery, Andechs) depending on how much time you have after visiting the castles you could visit a few of them on your way to Munich.

Chris, I like all your suggestions except one. Where did you stay in Reutte? We weren't impressed by it, much preferred over the Austrian/German border in Fuessen. Were you with a group?

That's a pretty standard Rick-Steves-route through Germany. It sounds like you have about 4-5 nights for the Rhine/Mosel and whatever else you see. I'd consider 3 nights there - if you're interested in castles, that's where you'll find the authentic knights castles, 800-1,000 years old: http://www.burg-eltz.de http://www.marksburg.de I'd suggest 2 more nights in the Rothenburg area. Not for Rothenburg, which only takes a day, but to see a bit more of the Germany that most tourists don't see. In Salzburg, Hallstatt, and especially in Füssen and R'burg, you'll be shoulder to shoulder with fellow tourists. A couple of days in Nuremberg, Bamberg, and/or Würzburg will give you window on German life today in some of its more handsome, well-preserved cities without the tourist trappings. Bamberg is especially fetching. A car for this trip isn't necessary. If train travel is a good idea at all, it's a fantastic idea in Germany, which boasts regular and dependable service and 5,500 train stations, 1,029 in Bavaria alone. It's also much cheaper to travel by train in Germany than elsewhere if you have the right information. There are regional daypasses throughout the country, like the 3-day VRM pass on the Rhine/Mosel that provides 3 days of hop-on, hop-off freedom for 2-5 people at 40€. A daytrip to the castles in Füssen (which are actually not castles but 19th-century palaces) is 29€ for 2-5 on a Bayern Ticket daypass. And you can use it on buses, trams and subway within Munich too. I've driven rental cars on multiple occasions in Germany back when cars were price-competitive with train travel, but not for any true reason, only because I wanted to drive at the time. I will only do so again if I book a mountaintop lodge in the deepest woods or become disabled.

Here's a map of the train lines just in Bavaria. The Bayern Ticket daypass can be used throughout the region, which stretches from around Aschaffenburg in the northwest (near Frankfurt) to Salzburg in the southeast. http://www.bahnland-bayern.de/content-startseite/streckennetzplan-pdf Bayern Ticket info: http://www.munich-touristinfo.de/Bavaria-Ticket.htm