We are planning a trip in Sept, from NY to Cinque Terre, to Sardinia. It sounds like the best way to get to Cinque Terre from NY is to fly into Pisa and take 2 trains. Is this confusing? I have a little fear of taking the trains, as I once had a bad experience at the train station in Rome (no one spoke English and I had no idea where to go, if I had to stamp my ticket,etc). Also, would I purchase the train tickets ahead of time? How would I then get from Cinque Terre to Sardinia? Do those ferries run every day in Sept? Then what would be the best way to get back to NY? I thought maybe ferry to Rome and stay over night? We have been to Italy many times, but never these locations. Would it be best to use a travel agent to help to figure out the trains and ferries? Is this trip feasible for 12 days or is Sardinia too far away from both Cinque Terre and Rome? It sounds like we may lose 2 full days on the ferries??

It's probably easiest to buy train tickets in Italy.
There are ferries from Genova and Livorno to Sardinia. Most of them are overnight, so you won't waste any days travelling. They are big ships with bars, restaurants and cabins. They will not be too busy in September so you shouldn't need to book far in advance.
www.moby.it
www.gnv.it
www.corsicaferries.com
www.tirrenia.it