Better choice of train routes plan A or B?

Yes we do plan to use the bus I was just wondering if it was better getting Venice from Milan or going back a little to Florence?

I would stick with A, as the stop in Florence breaks up a somewhat long trip from Cinque Terre to Venice. Going to Florence and taking the bus to Siena will not be efficient for your itinerary. There's a 10:04 train from Orvieto to Siena (change in Chiusi) that takes only 1:47, and is cheaper and much faster than going via Florence. Also take the train from Siena to Cinque Terre to avoid backtracking to Florence on that leg of your trip, saving more time and money. For your itinerary, the benefits of the trains outweigh the slight inconvenience of needing to take a local bus to and from the Siena train station.

Thanks Frank I was second guessing myself

I agree with taking the train to Siena. It's not that hard to catch a local bus from the station to your hotel. (Although I would recommend printing out a map of where your hotel is compared to a landmark.) And don't be afraid to ask the bus driver to help you know where to get off.