I really liked Brno, in the east of the Czech Republic, That’s on the main line between Prague and Vienna.
Many people recommend Cesky Krumlov as a beautiful town to visit. There are direct/ indirect trains from Prague (if you change at Ceske Budejovice, the short trip to Cesky Krumlov isn’t covered by the pass), and decent onward connections to Austria.
Between Austria and Paris, you have a lot of options. Obviously there’s sleeper trains, which are very time effective. But I’d recommend Salzburg and the Tirol as places to visit. In the Tirol, I stayed in the Oetz Valley, which is well linked by bus (not included) from Oetztal ÖBB station. The valley is gorgeous.
If not taking the sleeper to Paris, I would continue through Switzerland. Very efficient transport. You can cross the country on the scenic railways if you have time, such as the Goldenpass.