Congratulations to your daughter on her graduation. No worries; you can have a very nice trip to Wengen and Lake Como but I will suggest a few adjustments.
I would not recommend flying to Zurich; that actually does not actually leave much time, if any, by the time you build in adequate time between you landing in Milan and the departure of your flight (lots of time in case your plane from the US arrives late. Then you fly to Zurich, and it is still another 3 hours or more before you get to Wengen.
There are alternate routes to Interlaken Ost, the gateway to Wengen, that would be faster than that. I or someone else can describe those, but I will start by suggesting you slow down and break up the journey with an overnight in lakeside city en route to start your trip off right. The first that comes to mind would be to go from landing at MXP to Milano Centrale by train (roughly 1 hour), transferring there to a train heading to Locarno, a Swiss town right on Lago Maggiore (2.5 hours away).
The train station there is close to the lakeshore and you can stay overnight in a hotel closeby, right on the lake if you wish. If your plane is reasonably punctual you should have most of the afternoon to stroll the lakeshore and even swim (chilly water this early). This lakefront hotel has rooms available for 12 June:
https://www.hotelgeranio.ch/en/
Next day, you take the regional train (oddly named with the acronym FART, which you will see on the schedules) to Domodossola; this is the famed Centovalli railway on a scenic route. At Domodossola you pick up the regular train service into Switzerland, heading to Interlaken via Spiez and Brig. There are trains that do this without a change at Brig if you want to minimize changes. Travel time Locarno to Interlaken Ost can be under 4 hours if you take an afternoon train (for some reason the morning trains take longer, at least on the June 13 schedule).
Becasue you are traveling the day after your flight, you can schedule this journey with certainty, and buy tickets online now to get the best price and the schedule of your choice.
There is also an option to go from Locarno to Interlaken via Luzern, but I am saving that for your return to Italy. Before you decide on Varenna, make sure you can find suitable lodging there. It is a small town and some places do get booked up, but maybe midweek in June you will be OK.
Assuming you do stay with Varenna, you can reach the town via Luzern by taking a train from there toward Milan, on the scenic Gotthard Pass route. You can either go as far as the town of Como and ride a lake ferry up the lake from there (slow), or stay on the train to Milano Centrale and change there to the train heading to Varenna, 1 hour away.
Then end your trip with a night in Milan before flying out from MXP. No need to put Milkan in the middle with 2 nights there. Your time is better spent in Wengen and lakeside.
Note that some will suggest you take the Bernina Express route to reach Varenna directly from Switzerland without going to Milan. However, this involves a long travel day from Wengen to Pontresina to catch that train. And when you reach Tirano there is another construction interruption in the tracks, with a bus replacement between Tirano and Colico on the way to Varenna.