Bob, I hope that this will be a very interesting and beautiful trip for you.
The only area where we will be that might be of some concern is southern Bavaria...
After extreme spells of rain and thunderstorms we had major floods and landslides throughout the Alps. The catastrophe hit Switzerland, Austria (Tyrol) and Southern Germany (Bavaria). All in all, in many villages in the Alpine valleys thousands of houses were destroyed. But you can relax - although in certain places the damages still are very visible, almost all traffic lines (road and rail) have been repaired. The international lines are all open again, so your trip will not be disturbed.
However, on your RR trip through the Alps (Florence - Brenner pass - Innsbruck - Salzburg - Munich) probably you will note some fresh scars along the mountain slopes. Well, that's another way of 'Mother nature' to show us, who's the real boss on this globe!
But you're really in for a beautiful rail trip. I don't know the Czech and Croatian railroads, but I know by experience that the international passenger trains of the the other countries (Italy, Austria, Germany) are great to ride. You also made an excellent selection of some very beautiful cities to visit. Enjoy your stay in merry ol'Europe!
Ron