Dana,
I tend to agree with David. This is a very short trip and while it may be possible to fit all those stops into your Itinerary, it's a bit "ambitious" IMHO.
I'd also suggest open jaw flights, but given the circumstances with the "miles", return flights from Milan will also work.
I'm assuming you'll depart on 3/18? You'll normally arrive the day after you depart from the U.S. Although some people aren't badly affected by jet lag, I've found that it's a good idea not to underestimate the effect. On some trips I've adjusted easily, but on others it has taken several days. For me the adjustment after returning home is usually worse.
I'd suggest dropping both the day trip to Pompeii and the side trip to Pisa. The trip to Pompeii from Rome is a LONG and tiring day, and there's more than enough to see in Rome. If possible try to allow more time in Florence than a "stop-over" as it's also a wonderful city with lots to see. Spending several hours on the train for a short visit to the Tower is not really practical. As Rick says "assume you will return".
To answer the question in your last post, taking a day trip to Varenna / Lago di Como is easily possible. I used that method to make a return visit to Varenna in June. If you take an early train and then the last train back to Milan in the evening, that will allow a full day for touring not only Varenna but also a side trip to Bellagio if you're so inclined. That would also allow a fine meal at Albergo Olivedo before heading back to Milan (it's only about a 10-minute walk from there to the station).
You might want to pack a copy of the Italy Guidebook along, as it has lots of suggestions for good lodgings & restaurants, transportation info, sightseeing info, etc. I find it a good source of reference when travelling (you'll see those blue & gold books ALL OVER EUROPE!).
Good luck with your planning & happy travels!