Lyon - Milan - Cinque Terra - Pisa - Florence - Rome

Before buying a railpass, compare its cost to point-point tickets in Italy. To compute the cost of point-point tickets, use the Trenitalia website. Understand that when using a railpass in Italy, EuroStar trains require a significant surcharge (€15-€20), called a reservation (see here) because seat reservations are included with the surcharge. Without doing a detailed analysis, I can't say for sure, but my gut feeling is that point-point tickets for your Italian route would be less than a railpass plus reservations.

Check Easyjet for flights between Lyon and Rome. Just be sure to note that the flight from Lyon is to Ciampino Airport rather than FCO. Ciampino is a little farther out but a bus runs from there to the Termini train station in Rome.

For the rest of your trip I'd look at point-to-point tickets on the train.

If you plan ahead, point-to-point tickets will be cheaper than a railpass for your routes.

If you book well in advance (up to 90 days allowed) at www.tgv-europe.com, you can get discount train fares for either Lyon-Chambery-Milan or Lyon-Geneva-Milan. To keep the site in English and to avoid being bumped to the Rail Europe site which doesn't offer discount fares, choose Great Britain as your country of residence. Pick up your tickets at any SNCF station in France.

Since the Trenitalia site doesn't accept US credit cards for onlne booking, buy your Milan-Cinque Terre-Pisa-Florence-Rome tickets when you arrive in Milan. If there are enough days between your arrival in Milan and your trip from Florence to Rome, you might qualify for a discount fare for Florence-Rome.

As Sharon says, fly easyJet from Rome Ciampino to Lyon. Book ASAP to get the lowest fare.

Thanks for all of your help!