Berlin > Bamberg > ??? > Munich

If you like fortresses, visit Marienberg in Würzburg. If you like Fachwerk buildings and walled towns, Rothenburg odT is nearby. From Bamberg, one route south goes through Donauwörth. From there it's a short trip back to the north to Nördlingen, another walled city with Fachwerk buildings. A day trip from Nördlingen is Harburg, with an intact castle.

Personally I don't mind one night stops for destinations of this size and proximity - just be smart choosing your travel times.
Wurzburg > Bamberg > Nuremberg > Regensberg

Bamberg to Nuremberg is a quick, cheap VGN ticket away. If cold beer and light hiking are in your wheelhouse, try the Funf Seidla Trail in Graefenberg, north of Nuremberg by train.
http://www.vgn.de/en/hiking/seidla

If castles interest you, I think Germany's best is in Coburg, just up the road from Bamberg, although in the opposite direction of travel from Munich. Well worth a half-days visit if you can squeeze it in.

Würzburg and Regensburg are my two favorite towns in Germany.

Regensburg lies more directly on your way. I spent two nights there solo in 2012. Great town for walking about. Try the Kneitinger Brauerei Restaurant near Arnulf Platz for good German food and beer. I liked Pam Pam Pizzeria, especially after so many days of German food. We have had good food and beer at the Regensburger Weissbräuhaus on Schwarze-Bären-Str. I had a Helles rather than a Weiss Bier and it certainly was good.

The Regensburg cathedral and bridge were built in the 1140's, as was Wurstküche (good for wursts and beer) at the food of the bridge in the city. It was built to provide lunches for the workmen and is still going strong. Have a bid of history with your suds.

try the Funf Seidla Trail in Graefenberg, north of Nuremberg by train.

... and don't waste your drinking capacity at the first station: the very best ist the Lindenbräu in Gräfenberg.

Nuremberg!