We like doing a mix of big cities, and quiet laid back small towns /
pretty areas.
Black Forest: "laid back and pretty" but a sizable detour, and the Rhine/Mosel is more worthwhile on the whole.
Rhine / Mosel: Very "laid back and pretty" for the most part. It's not about choosing one town like Bacharach or Cochem specifically, but about the historical and cultural significance of the region over the centuries. The medieval castles, fortresses, and toll stations, the old-world towns, the dramatic landscapes, the outdoor activities, the river cruises, the wine culture, the footprints of Ancient Romans, and of course the retaking of the Westwall and the Rhine as the end of WW II approached... there's a lot to see and do here, and it's spread out over a fair amount of real estate. Like Berlin, a proper visit means at least 3-4 days in the area, not including the travel time to and from.
Salzburg: You might get away with just one night if you sightsee there on two days.
Rothenburg: 2 nights? A small and insignificant backwater compared with Salzburg. And extremely touristy - its only purpose today is to take in tourists. It was nearly half destroyed by WW II bombs but handsomely rebuilt after the war - not sure why Rick calls it "well-preserved" when so much of it was restored. Rick recommends it but also admits that it's "becoming a medieval theme park." You don't need 2 nights to see the town - a few hours are enough. But you could spend 2-3 nights there (or better yet somewhere nearby that is a bit more normal and laid-back, not so overrun by tourists) since there are lots of other attractive options in the area... Bad Windsheim's open-air museum… also Sommerhausen, Ochsenfurt, and Marktbreit, sleepy old-world river towns north of Rothenburg.... And not far away is one of Germany's nicest big cities (half a million population is big to me) - Nuremberg, which IMHO has a couple of big advantages over Berlin... it's close to your other destinations in Bavaria, and it has a relatively compact center where most of the attractions are located - you can see it in less time, and without using a lot of public transit. Like Berlin, Nuremberg has several WW II sites as well. With 4-5 days in the Rothenburg - Nuremberg region, you would have many great choices in front of you.
So I am going to suggest that instead of the constant checking in and out like a tour bus customer, instead of flying and driving around to so many different places, you stay in no more than FOUR different base towns for the 2 weeks you have...
Visit Berlin on some future trip when you can dedicate the time it deserves.
Fuessen is a mostly unnecessary detour that would repeat the mountain experience of the Salzburg area and take you to the very "unlaid-back" experience of visiting Neuschwanstein (for its overcrowded 30-minute tour, not of a true castle, but of a palatial royal residence with a fake castle exterior. Better to visit Nymphenburg Palace in Munich, perhaps, or maybe Herrenchiemsee Palace in Prien - also built by King Ludwig II, it's half way between Munich and Salzburg in a stunning setting, on an island in Lake Chiemsee.)