Itinerary help on our trip destinations, timing and advice on using only trains.

I would push the Alps (Austria, Bavaria & Südtirol) to the last two weeks in June. That's when more or less high season starts and there are wildflowers and most Alm are open. It can still be cool then in higher elevations, but comfortable and hot on some days. As always you can get some very rainy days in the Alps, but usually not more than half a day on any given day and sometimes thunderstorms. Was at the Obersee from Königssee a few years ago in early May and Fischunkelalm was not open yet and the cows were not out into the pastures.

I checked on your itinerary with the train routing and times just for my own curiosity. The closer you get near Switzerland the more complicated and long haul the train rides become. Driving might be best there. You might want to get a paper map and plot it out, because if your list is order you do some backtracking. For the long hauls you might figure in one stop along the way. Buses seem to take just as long, maybe there are some express buses like Flix. There might be some independent trains available. Weather seems to vary every year now, so just cross your fingers. April in Italy should be a good place to start. Bon Voyage!

I know we are showing some backtracking as we’re trying to do Italy first, then Germany and then the mountains because of the weather, seasonal closures in the mountains, snow levels. And yes we have a good paper map and use Rome2Rio for a high level look.

Is there any problem with car rentals crossing into 3 different countries?

I would shop the car rental companies and see what the current policies are or going to be next year. The one thing to make sure of is that your car insurance is good for your trip, and pickup and drop locations and times.