Germany intinerary

I want to see Berlin Munich Salzburg as well as perhaps a night in a smaller German town

Go to Bamberg; it is on the line Berlin to Nuremberg.

Speaking of trains, will the high speed train between Berlin and Munich be ready by then?

They've already run at least one train full of dignitaries. Testing is now in earnest and tickets go on sale next month for the public starting with the December 10 schedule update.
https://www.thelocal.de/20170616/new-high-speed-train-from-berlin-to-munich-makes-historic-maiden-journey

But the Sprinters won't stop at Bamberg, only Erfurt and Nuremberg.

Just throwing this out there, as it's not a small town nor on the Berlin-Munich line, but - have you thought about Dresden? I spent a summer there and loved it. The main attractions (including the rebuilt Frauenkirche, which was destroyed in the firebombing, and the Zwinger) are all pretty close to one another. You could do it as a day trip from Berlin, as the direct train gets you there in less than two hours. I posted something similar on a different thread, but I'll repeat it here: Salzburg was a disappointment both times I've visited. However, it was worth it to go on the Sound of Music Tour. Even if you aren't a huge fan of the film I'd recommend it, as it gets you up into the hills and the scenery is breathtaking. And Hallstatt is absolutely wonderful, if you want a small town to get away from the big cities.

I second the vote for Dresden. There is also Leipzig. We were in Dresden summer 2015, and Leipzig this summer. Both are smaller, less hectic, but very nice. Dresden is the capital city of Saxony, and has many wonderful artifacts from that era, including a wonderful treasure room. Leipzig has Bach and Bachanalia, as well as the Memorial to the Battle of All Nations (Napoleonic wars). Both were good. Rather than Salzburg (out of the way), I would do Berlin for 4 day, Dresden-Leipzig for 2 days each, and Munich for 4 days. Another option is to take an early-morning train to Dresden, stay the day, and train to Leipzig to stay for the night. Do Leipzig the next day, stay overnight, and go to Munich the day after. If you like Bach, seeing his grave in the Thomaskirche is a moving experience.

Dresden has magnificent museums. If you're not a museum person, it might not be the best choice, because the area rebuilt in historic style is rather small.

I haven't been to Leipzig, but I liked Erfurt a lot. It has a large, beautiful historic district and the liveliness typical of college towns. If you're into castles, Wartburg isn't too far away; it's in Eisenach, which also has attractive architecture. And the Buchenwald concentration camp just outside Weimar is a very worthwhile site to visit.

I would spend more time in Salzburg, we were in Germany Austria and Switzerland this past June and while I loved Munich, Salzburg was an amazingly awesome city, certainly a highlight for us.

Hi,

You do have a number of choices. I would suggest Leipzig, see the museums/houses of the famous composers.....Bach, Mendelsohn, Liszt, Schumann, Wagner that Leipzig has to offer. Historically, I suggest too the Völkerschlacht Denkmal, commemorating the battle of Leipzig in 1913 where the Allies were victorious over Napoleon. In 1945 the Americans got to Leipzig before the Soviets, reached the huge Völkerschlacht memorial, and received hostile fire from that direction. With that US troops just turned artillery loose on the memorial.

To reach it you take the S-Bahn from outside of Leipzig Hbf. Next to the Denkmal is the museum on the battle itself seen from the perspective of the Allies.