"Actual stops (cities we are exploring) are Amsterdam - Paris - Fussen - Munich - Salzburg - Rothenburg - Amsterdam"
Paris-Fuessen with a stopover in Colmar will involve 10.5+ hours on the train. Paris - Rothenburg is 7.5 hours, Paris-Munich about 6.5. It's a long way to Bavaria from Paris. Long trips however you slice it. Have you thought about stopping over near Mannheim - which is just 3 hours by direct train from Paris? Or near Frankfurt, which is just a bit further? You can change in Mannheim for some interesting places nearby - Heidelberg, Speyer (the Technik museum there is amazing - check it out) Worms, Neustadt-an-der-Weinstrasse, and Mainz are all worthy destinations on the route to Rothenburg that aren't on the tour bus trail (Rothenburg, Fuessen, home of the faux-castle Neuschwanstein, and Salzburg) but offer a very good look at Germany. I also suggest you take a look at Wuerzburg and Bamberg (not far from Rothenburg) both of which are UNESCO World Heritage sites.
Also, I suggest doing some research on Christmas markets, which will be in full swing during the last week or so of your visit. One that comes to mind is Ruedesheim's - in Germany's castle-studded Middle Rhine Valley, on your way north to Cologne and Amsterdam.