Switzerland, Italy & Austria April,May or June 2025

Congrats on the retirement. Is this your first trip to Europe?
Just some random thoughts.....
Many mountain lifts and trails don't open until mid June.
With the increase in tourism post- pandemic, it's highly encouraged to book lodging in advance. There are no shoulders seasons any more. And, 2025 is the year of the Pope's Jubilee, bringing millions more visitors to Rome. Also, avoid everywhere the weeks before and after Easter.
You will have more flight options flying into Munich. It's an easy 1.5 ht train ride to Salzburg. Where are you flying from?
What does your "list item" mean?
Plan in terms of nights, not days.
Have fun planning. Get some guide books, review the Trip Reports here, read the posts under the specific countries, look at Cameron's blogs here, and join area-specific Facebook groups.
Wishing you a great trip.

You absolutely should not just do lodging as you go. You’ll spend way too much time trying to find availability and probably won’t end up with the best options.

You can take the direct train from Salzburg to Zurich and stop in Innsbruck along the way. Luzern is also worth seeing on your way to Mürren.

Maybe something like….
Salzburg - 3 nights
Innsbruck - 1 night
Luzern - 2 nights
Mürren - 3-4 nights
Zermatt - 3-4 nights
Venice - 2 nights
Florence - 2 nights
Rome - 3 nights

There is plenty to see in the surrounding areas around Salzburg (lake district Salzkammergut (places like Halstatt), Sound of Music tour of the countryside, castle, etc,) so having a few nights there to start your trip, get over jet lag, etc will be nice.

Another option is doing this in reverse. Do your Italy big city things first and then get into the more mellow Switzerland and Austria. That’s personally what I would do, as Italy is extremely congested and a bit overstimulating to me. I’d be in Rome just wishing I was back in the Alps :)

Why did your friend say you have to go to Salzburg? It would be different if it weren’t an outlier but it is. Salzburg is best if visiting Munich, the Bavarian Alps and Vienna. I suggest sticking with your original plan. You will lose two days traveling two and from Salzburg that involves multiple train connections. There is nothing fun about hauling luggage when transfers are involved.
When visiting mountains add an additional night in case the weather doesn’t cooperate. There is a lot to see and do in both Zermatt and the Lauterbrunnen Valley so I recommend five nights in each place. This leaves eleven nights for IT which isn’t much.
Venice deserves three nights, Florence three nights and Rome plus Vatican City needs four nights. Cut out Milan because it’s a lesser site and you do not have time. Don’t spend most of your time riding the rails going from one place to another; that will be boring.

Thank you for your help. We will probably change and go to Rome first (before Easter) then head north..

Welcome to the forum, and to the club of happy retirees with time to travel. I am afraid there is going to be some rain on your parade, as you can see, but it is all with the best of intentions, so you can plan a fun and realistic trip with minimal hassle.

First the good news: neither the Glacier Express nor the Bernina Express will be closed during yout time fram. The Bernina Express has a short section that will be closed for a few days in early April, and again for a week in May (the &th to the 14th). It should be easy to schedule around that, but if not, there is a replacement bus service to bridge the gap.

https://tickets.rhb.ch/en/pages/bernina-express

The annual Glacier Express closure in in October to early December; in April and May it will be running on the regular schedule. However, cannot get reservations until 93 days ahead of your travel date. And you should get them as soon as they open up, so make that date on your calendar as soon as your travel dates are firm. You can wait to buy the actual tickets until later, as if you get a Swiss Travel Pass you won’t need a ticket, just the reservation. If you decide on Half Fare Cards, then you will buy a ticket. Or if you get neither pass you can still save money with a Saver Day Pass (which can be explained later if you are interested).

https://glacierexpress.ch/en

As noted above, the Jubilee year will make Rome and the Vatican particularly crowded in April, especially around Easter. If you wish to start your trip in Rome, I suggest you plan to leave Rome and head north to Florence, etc. a few days before Palm Sunday.

With both the Bernina Express and the Glacier Express on your wish list, the logical order of travel, should you wish to start in Rome, would be Rome—Florence—Venice—Milan—Varenna on Lake Como (or Tirano, where you pick up the Bernina Express. That’s Italy. Then for Switzerland, Tirano—St. Moritz (most forum members advise staying in the more charming nearby village of Pontresina instead)—-(Glacier Express) Zermatt—-Berner Oberland (might be hard to find lodging in Gimmelwald in April but nearby Wengen, on the other side of the valley, should offer something). From here to take the train to Zurich, spend the night there, then the direct train to Salzburg. Fly out of Munich to save backtracking.

Zermatt will be quiet but not “shut down”. It is a village and people live there. Plus there is skiing on the glacier year-round. Most lifts close but the the lifts to Matterhorn Paradise are open. And somewhere I saw that the link to Cervinia ran until May 5 in 2024, so there is hope for that one too.

I would strongly urge you to make advance reservations for hotel everywhere. Essential in Italy that time of year, and advisable in Switzerland as well. You are going to be tied to certain dates for the Glacier Epxress anyway, so have no flexibility possible there.