City Night Line (7-Days on Overnight Trains)

I think there are a number of things to consider.

Showers: I believe those are not deluxe sleepers, i.e., they do NOT have showers in the compartment. The showers would be at the end of the car and shared with everyone. Some train stations might have shower facilities (I know Munich does).

Luggage storage: I don't think that is one single train for the whole week. Rather it is a series of different trains. Hopefully all the stations will have luggage storage facilities.

Note, you can set up the schedule with any number of extra days in each city, so you could take the train one night and then have a hotel the next. That might somewhat solve the above questions.

You can only book the 7-days nights package by phone, so maybe you can get some of the questions answered. I would be good to make sure you can get adjoining 2 person compartments since the sleepers are for 2 or 3 people, only.

Just be aware... while some people can get an adequate rest on a night train, the majority opinion on this site appears to be that getting enough sleep on a night train is difficult, and that frequent night trains can leave you exhausted during the day.

I looked at that ever-so-briefly and decided I didn't like only having 1 day everywhere. 1 day for Paris and 1 day for Hamburg? They're both fine cities, but come on...

Also, they design the schedule so as to have extremely long train journeys. If you rearrange the cities in geographical order, you'd have Berlin-Hamburg-Copenhagen-Cologne-Paris-Zurich-Munich. Plus a lot of extra time not on trains. (and hotel expenses to be sure, but you're not tied into spending 13 hours everywhere)

Check what time the train arrives/departs to get a good idea of how much sleep you can possibly get, keeping in mind that train sleep is around 80% as good as regular sleep. And watch out for trains that arrive before 8:00. I consider myself to be a morning person, but that's just deadly.

Some travelers don't do back-to-back night trains because of the exhaustion factor from two straight nights of not so great sleep. Other travelers--those who are pretty good sleepers I guess--try to maximize use of night trains in order to get from point A to B at night. Rick is one of the original night train guys and to this day (see ETBD 2009) recommends maximizing use of night trains--but I wonder, now that he's not quite as young as he used to be, if he himself still does much back-to-back night trains (what about it, Rick?).

Here are the cities I'm wanting to visit ... following a Reformation Trek (Martin Luther/John Hus), and trying to work other cities into a "short" marathon. How much time, and what would you recommend, and do I need to cut anything out to not go over seven days/nights (don't laugh, please; lol)?
Reformation Trek (Have to):
Wittenberg
Halle Saale
Eisleben
Erfurt
Eisenach
Weimar
Bamberg
Rothenberg
Heidelberg
Worms
Mainz
Rothenberg
Augsberg
Constance
Lucerne
Zurich
Interlaken
Bern
Montreux
Geneva

Would Like to:
Berlin
Munich
Salzberg

Um, so you've listed 21 'must do' cities and 3 'would like to do' cities over 7 days. Plot them on a map and see what order makes the most geographic sense. Then figure out which of those cities has train service. Then pick a few good home bases.

But be careful: 3 cities per day (3.5 if you include the like-tos) can quickly turn into a deathmarch (deathride) and you'll be spending a fortune on lockers if you bring your luggage along each day.

Chop out cities that don't fit into your map/schedule unless they're a must-see. I don't know how long your stops will take, but assume 2 cities per day is a reasonable maximum, not counting Munich, Salzburg, and Berlin (each worth 1-3 days on their own). Try to stay in the same place for at least 2 nights (a new hotel every day just isn't fun).

Since you have a lot of small towns on your list, maybe renting a car would make more sense. Parking in small towns is easy and inexpensive, and no luggage storage issues.