My wife and I are arriving in Zurich at 07:50 and leaving from Milan at 10:25 12 days later. Our current itinerary goes something like this. Take the train straight from Zurich to Lucerne for 2 nights. Travel up to Wengen or Murren for 2 nights. Take to train to Cinque Terre and stay in Monterosso or Vernazza for 3 nights. Take the train to Sorrento for 3 nights then back to Bellagio for the final 2 nights. I am concerned that we will be spending to much time on the train. I'm thinking that the trip to Sorento and Amalfi Coast might be putting to much on our plate for 12 nights. Any thoughts or suggestions,advice etc would be very helpful.
It sounds like your flights are already booked. If so, I would leave out Sorrento/Amalfi Coast and save it for another trip. I would stay in Milan on the night before departure in case there is a train strike, and also because your flight leaves in the morning.
You have good instincts. Drop the Sorrento link and add those nights elsewhere. Do not add another location. If you love the mountains, and particularly if you are hikers, stay 4 nights in the Wengen/Muerren area and maybe one more at Bellagio for a relaxing end to the trip.