"Would you be in favor of skipping Munich for Numberg? (Nuremberg)... Our daughter mentioned a concentration camp so we thought of Dachau but we could always keep 5 nights in Berlin and do one there."
5 nights in Berlin, w/ day trip to Sachsenhausen concentration camp, is probably OK. Munich is a rail hub and you may have to pass through there for Salzburg, but there's no law that tourists must overnight or sightsee in Munich; yes, I'd favor Nuremberg over Munich, especially since you have no firm plans for your stay there. The WW II options ... the art (and other) museums... the Imperial Castle complex... the attractive old town zone (yes, with half-timbered buildings)... the churches... the beer pubs... the Handwerkerhof... It sounds like it would meet your needs - actually I think there's something for just about everyone there. And Nuremberg is actually a better "jumping off point" for you than Munich anyway if Rothenburg will remain a target - it's a doable day trip from Nuremberg by regional train and costs only €20 for the family (that is, if your daughter is <18) on a "Tagesticket Plus" day pass (buy at station on day of travel.) (I find the Nightwatchman shtick and the torture museum stuff more than a little hokey and R'burg too touristy and theme-park-like overall - and you can see half-timbered buildings in all the Rhine towns too - and there are better day trips from Nuremberg IMO - but admittedly, my R-burg take on this forum is in the minority.)
Possible trip organization for major train trips with Rhine and Nuremberg on the itinerary: it might be convenient to fly into FRA and out of MUC...
FRA airport - Rhine: 1 - 1.5 hours
Rhine - Nuremberg: about 4 hours
Nuremberg - Berlin: 3.5 hours
Berlin - Munich: 4.5 hours (lunch + sightsee in the afternoon if you have any specific goals there) + Munich - Salzburg in the evening (1.75 hrs.)
Salzburg - Munich in the evening of your final day: 1.75 hrs.
Munich - MUC airport: 40 minutes
I'm sure there are other options for ordering as well.
Of course you then also have day trips to Sachsenhausen, Berchtesgaden, Rhine towns, maybe Werfen and Rothenburg.
A German rail pass of some sort for the big trips might be in order for convenience, for possible changes in your plans, and possibly for savings. The short trips can be done by local day pass or possibly by rail pass (if the additional cost per travel day is competitive.)