Julie, I like your revised itinerary, with the following reservations. observations and suggestions:
Too much time in Milan. It has the least "atmosphere" of all your towns and cities and there really isn't much in the way of tourist sights. How many performances at La Scala???
Then move on to Verona which is really worth at 2 days if you can. Otherwise, spend one night, then take an early train to Padua, leave your bags at the station and spend the day, then continue to Venice.
I guess you could go to Verona as a day trip from Milan, figure 3 hours for the round-trip train, and be back in Milan in time to change for the La Scala performance. How much will you enjoy it if you've been on the go all day? How much time will you have to sightsee in Verona? You still have to get to the sights from the train station, and back again. Dinner?
Venice needs at least 2 full days, which I think you have. If you can, think about adding another day.
Pisa is very easy to see on the way from Florence to CT. I had to change trains there anyway. Take a taxi from the train station, so you don't waste time looking for the bus stop and waiting for the bus. If you want to climb the tower (quite an experience because the ramp tilts so much) you have to reserve in advance. The church and baptistry are worth seeing.
Except in the CT, I found elevators at all the train stations on your route, or the platforms were at street level.
Have you considered dropping Assisi? While it's only about 1.5 hours on the train from Rome to Florence, adding a day in Assisi adds almost 4 hours just to train time, plus the hotel change. So you are losing most of an entire day of sightseeing.