Train Travel and Itinerary for Northern Italy

You might consider booking some of these in advance to travel more comfortably on Freccia trains and save a bit of money, but you can ride them at full price spur of the moment if you like. You can also travel on Regional trains, more stops and maybe more connections and no reservations. Varenna to Milan and Malpensa is all by Regional trains, so you don't need to book them in advance.

If you want to shorten time in Varenna to add a couple nights at an additional location as you mention, some easy possibilities might be Padua (on the way from Venice), Verona (you whill change trains there going to and coming from Bolzano), or Bologna. Other cities in Emilia-Romagna such as Parma or Ravenna would also be easy additions. You could also spend time in Milan.

I did not mind at all taking the regional trains and found that I ended up choosing the flexibility of the regional trains (no reservations) over the relatively small amount of time saved by the faster trains for routes like the ones you listed where you will be changing trains at least once.

The regional trains from Varenna to Milan Central are often very crowded, and can be SRO. Since the only option is a regional train, there are no seat or general reservations.
Once at Milan Central, you'll take the Malpensa Express train ( or bus) which takes about 50 minutes. In our experience, sometimes the airport trains are just canceled. There's about 40 minutes wait until the next train, if my memory is correct.
I am assuming you're flying out of Malpensa and not Linate, correct? There is a smaller airport in town, Linate, which is much easier and quicker to get to, and many major carriers go into Linate.
Enjoy your trip, and safe travels!

I would shorten the time in Varenna, mainly because it's so darned crowded in the summer these days. And Venice is as well, but at least there you can get away from the crowds by getting out of the center. If you haven't been to Venice before, I would add nights there and/or in Ortisei rather than add an additional location.

We have been to Venice several times but since we are flying into Italy there, we couldn't leave without spending a couple of days in that special place. I've heard from several people about how crowded Varenna is in July. Would you recommend a different place on Lake Como instead? We just want to stay somewhere that has a train stop since we won't have a car and we remember enjoying Varenna on a Rick Steves tour we took many years ago (10+) as being an enjoyable place to stay.

In order to enjoy our time in Ortisei without a car, we were planning on taking some day trips to some of the nearby small villages like Castelrotto by bus. In Varenna, we planned on taking ferries to explore other places on the lake. Does that make sense?

Right now we're thinking about spending 2 nights in Bolzano rather than just one.

One issue I see with so much time in Varenna is that, unlike Ortisei, it is not at altitude, so there is a significant risk of persistent heat in the summer. There aren't many indoor sights in Varenna or the mid-lake area in general, just a few fancy villas that don't take a great deal of time to see. At the least, I'd recommend doing some research on the museums and other indoor sights down in the town of Como, just in case you run into this sort of thing:

Varenna weather -- August 2024

For all I know, August 2024 may have been the hottest on record, but it did happen (and I lived it for a few days in late Aug/early Sep). Use the pull-down box at the right, above the graph, to check the actual month you expect to be in northern Italy, and look at the most recent five years rather than relying on statistics from just this year.