Itinerary tweaks or suggestions

I think there are better (and more scenic) places than Rothenburg, that would be more in the line of what you seek. Its a nice place to visit, but since you're headed to Rome, I'd look for the German Alps (Garmisch, Fussen) or even Switzerland. I'd even skip Munich for the little time you have to spend there.

Thank you for your feedback, I have also learned the Night Watchman tour will not be running in Rothenberg which was one of the main reasons for including it - I will look to the German Bavarian area instead such as Fussen that you suggested...

Hi breyeo. You might consider Cesky Krumlov as a stop for a night or two between Prague and Salzburg, then to Munich from Salzburg. CK is very touristy, but fun. Cool castle and gardens above town, and if weather is right and you are interested, there is an easy, scenic kayak trip directly from town.
Enjoy your trip!

I'd personally spend more time in Munich and skip Rothenburg. Go on a day trip to Nuremberg or Regensburg.

From Prague to Salzburg is a little difficult you've got to take roundabout ways of getting there on the ground often with numerous buses and trains. Major highways don't go between those cities. There are a number of reasonably priced Cesky Krumlov shuttle services that carry people throughout the entire region in vans. You could have them pick you up in Prague and take you to Cesky Krumlov. After spending the night in very scenic C/K, you could have them drop you off in Salzburg.

Given the choice of cities, I too would bypass Rothenberg and spend the time in Munich--a great large European city with so much to see.

Munich to Rome is over 550 miles (and 10 hours by train)--a long way. Most say it's better to take trains into Italy during the day as the Alps scenery is simply magnificent. But 90 minutes on a plane sure beats 12-14 hours on a train. And you could have a 1/2 day in Rome which is precious time. ITA Airways and Lufthansa both fly Munich-Rome.

When you go out to Civitavecchia, you can take a train from Rome Termini. It's something like 45 minutes and trains are hourly except on weekends when they're every 2 hours.. In the Civitavecchia train station, you can catch a short taxi ride or a bus if you see one going that direction. It's maybe 1.5 miles to the port. There you will get on a port bus and for a short ride out to the ship for departure..

Will you leave day 11 on your cruise ? I would plan on at least 2 full days in Rome if you haven’t been before. I’d fly to Rome rather than take the train

Keep in mind that going by night train "Night Jet" from Munich Hbf to Rome requires one or maybe two transfers, usually in Verona or Venice.

Munich is a night train hub, I never went south on the Night Jet , only north or east. You certainly can do that ride with the first leg by night train from Munich. I would do likewise.

What time of the year is this trip?

Thank you everyone for your feedback and thoughts! We are doing this trip in late March - we will have 2 full days in Rome once we arrive and have been to Rome before so we are okay leaving the current amount of time there. I will be definitely cutting out Rothenberg as everyone suggests and will look into how to best configure the Salzburg and Munich sections - we want to leave the nightjet as we do have the OBB direct and we got the last sleeper car - we leave at 8:09 pm from Munich and arrive in Rome by 10am - only doing this as we got a full sleeping car so looking forward to the experience - now just have to figure out how to fill the days between leaving Prague on the 21st and heading to Rome on the night of the 27th.... we want that Bavarian experience.