Best transportation from Vernazza to Siena via Pisa and Assisi

The first step when planning an itinerary should be to look at a map. If you don't have one google maps will do. Pisa is along the train line from Vernazza to Siena (it's actually a station where you will change trains) therefore it's a perfect opportunity for a quick stop to visit the leaning tower. Then from Pisa you proceed to Empoli where you change trains again and take a train to Siena.
Assisi is out of the way (check the map) and you need to leave it for another day.

Thank you for the quick reply. We knew Assissi was out-of-the-way but it will be any time we go there with our current itinerary, it is an important stop for our group.

So I assume you are suggesting we make it a day trip from Siena or would it be better to do on our way to Rome assuming we continue to make it a priority to go there?

Deb,
You should be able to do the Pisa trip on your own on the way to Siena.

Vernazza-Pisa Train 1H29m There are luggage storage lockers @ Pisa Central station

Bus to Field of Miracles/Return bus to train station

Train to Siena 1H44m

For Assisi Viator has a combo tour

http://www.viator.com/tours/Siena/Assisi-and-Cortona-Day-Trip-from-Siena/d944-5919ASSISCOR

To try to combine both would be brutal

From Vernazza to Siena it's a 3.5-4.5 hour trip. Add a couple of hours for Pisa and more than half day is gone. From Pisa to Assisi is at least 4.5 hours by train. I don't know how long you intend to spend in Assisi, but to make it back to Siena you would probably need another 4 hours, when everything is factored in. There is a bus from Perugia to Siena, which would be quicker, but it's only one a day and you need to go to Perugia to catch it. Obviously Assisi isn't doable on the same day with public transportation.
The best would be to have a rental car in Siena and drive from there on a day trip. You can drive from Siena to Assisi in less than 2 hours.

Thank you so much for the thorough explanation!!

Can your group spend a night in Assisi on the way to Rome? There are so many important sights in Assisi, it's difficult to fit them in on a daytrip, especially using public transportation. There are a couple of trains per day from Assisi to Rome that don't require changes. A car would be most convenient, there are public parking garages in several areas near the historic center.

Or, have you considered a guided tour from Siena to Assisi, or arranging for a guide to meet you in Assisi (if you decide to drive)?

Those are good ideas for our group to discuss.
It seems if we decide to do both on the same day, our only option is an early start from Vernazza by train ( we get up early!) quick look at leaning tower of Pisa and then hire a driver to Assisi then Siena. Your suggestion of more time in Assisi is worth considering to go there on a separate day. Thank you for taking the time to respond.

"There are luggage storage lockers @ Pisa Central station"

There are no lockers at the Pisa Centrale station. Lockers were removed from Italy train stations years ago. Better yet, it's a staffed left luggage area. You luggage is stored behind the counter. We needed our passport to get our luggage back.

As for traveling from Siena to Assisi, I sense that its a "must" for your group. The public transportation options between these two cities is awful. As Roberto explains, it's a 4hr train trip with 2 train changes along the way. It's even more distressing when you discover that the two cities are only 80 miles apart. My wife and daughter did this recently but with a rental car. I don't know how many are in your group. I also don't know if you need to return to Siena or if you are heading off to another location. Either way, you can go to the Hertz office near the Siena train station and rent a car. Rent online in advance or there most likely won't be one. Also, it will most likely be a standard shift car and not an automatic unless you arrange otherwise online in advance. It's a 90 minute drive to Assisi. A couple of really nice and large parking garages in Assisi. Parking in the historic areas is limited to one hour.