Where to go after Munich Salzburg

So, you will have 3 nights in Munich? Sun, Mon, Tues. You seem to think you have 7 nights to work with. Either I am confused or you are counting wrong. If you have Sun, Mon, Tues, I would stay in Munich - plenty there for 3 days, with one optional side trip.

Sorry I have about 8 days to spend between the two cities.

Does that mean you arrive on Sun and leave not on the next Wed but a week later? I'm not trying to be difficult, just trying to get an idea.

I would probably go directly from Berlin to Salzburg. Salzburg is a 3 night place. If you wish, stay 4 nights, and do a day trip to Hallstadt. It is charming, but very small. We used Bob's tours - small van, 6 of us on the trip. Not the giant bus. In Salzburg, there is a great beer garden at one end of town. We went to a concert or 2 in town, inexpensive, elegant. The Mozart Birth museum is very interesting, and we enjoyed that a ton. If you like Mozart, of course. There's the cathedral, the fortress, etc. Plenty to do.

If you have 8 nights, you have 4-5 left. Then go to Munich for the remaining 5. There are lots of small towns in the area, which you can visit on day trips. We went to a town called Haar to visit a group that has a history of my mom's ancestors. Small town, not much to it. Probably if you go to Tourist Info in Munich you could find a charming town in the area. There is plenty to do in Munich. The English garden with the CHinese Tower Beer Garden, the day trip to Neuschwanstein, etc.

Don't go straight Munich maybe go to Bamburg or Nurenburg on the way. Play it by ear when you get to Munich. You may find it not that engrossing so you maybe can take a day trip somewhere else

It depends on what you like to do. If you want to visit King Ludwig II's castle in Füssen, that would be worth it (as well as the castle he grew up in a km or so away, Hohenschwangau). Nürnberg is a must. There are various castles in the area if you like that. Just outside of Regensburg is Walhalla, a classic Greek style housing the busts of people who have contributed to German culture (so they now have non-Germans in it as well). You like might also be able to sneak in a trip to Innsbruck (check out the oebb.at site). But you could also spend time in Berchtesgaden or the Fränkische Schweiz or go over to Passau. It depends on what you like.

Spend a few days in Thuringia, which is between Berlin and Munich. Erfurt, the capital of Thuringia, is on the direct train route, and a good base. The city offers one of Germanys best and biggest preserved town centres. Rick Steves liked it a lot:
https://www.ricksteves.com/watch-read-listen/read/articles/erfurt-simple-unspoiled-germany

From there you can do day trips to Wartburg castle and Weimar. The Wartburg is Germanys most important castle, a World Heritage Site, and the inspiration for Neuschwanstein. Weimar was the cultural capital of Germany in the 19th century (Goethe, Schiller, Liszt, Nietzsche and many more lived there), it's a pleasant small town with a preserved centre, a castle and a park, and it is a World Heritage Site too.

If you want to keep it simple, just take a day trip from your Munich base.

Landsberg is a Romantic Road town of 28,000. It's 45-50 minutes by train from Munich:
http://www.landsberg.de/web.nsf/gfx/SLL07-E_web.pdf/$file/SLL07-E_web.pdf

Landshut is only 40-45 minutes, a bit larger than Landsberg, quite a nice place:
https://www.hotel-cristallo.de/a_media/content/blog/194-historisches-landshut/194-historisches-landshut.jpg
http://www.landshut.de/en/portal/tourism/see-wonder-experience/sightseeing.html

Regensburg is larger yet, though not nearly as large as Nuremberg, and has a UNESCO World Heritage old town. Figure about 80-90 minutes.
http://whc.unesco.org/en/list/1155
https://tourismus.regensburg.de/en/about-regensburg/sightseeing.html

All 3 of these destinations are reachable on a day pass - a Bayern ticket in the case of Regensburg or a cheaper Regio-ticket for Landshut or Landsberg - both can be bought at Munich's main station from a ticket machine.

And almost no one goes to Landshut (relatively). It's a great location. You could also check out Wanderwege (walking in the woods). For example check out: https://www.bayern.by/wandern-in-bayern I'm not particularly recommending this website btw but these are easy to find with the walking/wandering routes clearly marked and online there are interactive (as a boy we had books of these and there still exist).

Recommend a day in Rothenburg ob der Tauber and at least a day trip to Dinkelsbühl.