First, I would like to thank everyone for their help. Right now I am drafting a rough itinerary so I can get hotel rooms booked. The actual details of the days will come together later. We're traveling peak season (mid-late June) so the hotel bookings are somewhat urgent.
Here is what we have so far and I am particularly looking for help in figuring out where to stay after Salzburg (day 11 onwards).
We prefer 2 nights in a place, but am not opposed to moving as I do have a deadline to get to Berlin for a conference.
Day 2 - Pick up car from Cologne train station. Drive from Cologne to Boppard. Leisurely drive, stop along the way at whatever strikes our fancy. Overnight Boppard
Day 3 - Explore Rhine region (likely do a cruise). Overnight Boppard
Day 4 - Burg Eltz (possibly Cochem) and drive to Rothenburg. Overnight Rothenburg
Day 5 - Explore area around Rothenburg (possibly Wurzburg). Overnight Rothenburg
Day 6 - Drive down to Fussen with stops along the way. Overnight Fussen
Day 7 - Explore Fussen area (palaces). Overnight Fussen
Day 8 - Drive to Munich area. Overnight @ Hotel Grunwald (free parking, just outside city centre, close to train station....I don't want to deal with parking in the centre)
Day 9 - Munich. Overnight @ same hotel.
Day 10 - Munich/Dachau. Overnight @ same hotel.
Day 11 - Drive to Salzburg. Explore Salzburg (yes, I know it's quite a drive...so it'll be an early morning departure). Overnight in Salzburg (no idea where yet).
Day 12 - Depart Salzburg...to where? Regensburg? Nurnburg? Landshut? Help!
Day 13 - Continue driving toward Berlin. Overnight in Erfurt???
Day 14 - See day 13
Day 15 - Must be in Berlin early morning to drop off car.
Day 16 - 20 - Overnights in Berlin at conference hotel.