Italy rail travel

Starting at the beginning. "what company/train (Eurorail or ??)". For most train journeys in Italy there is only one passenger train company: Trenitialia. They run 90% of the passenger trains in Italy. There are some local companies, but I don't think any of your proposed trips are in their areas.
Eurail does not run any trains, it is a US-based travel agent which sells tickets and passes for many different railway companies WITH A MARKUP, cheaper to buy direct from the company running the trains (in this case Trenitalia).

Trains in Italy are relatively cheap. It is usually much cheaper to buy individual tickets than to buy a pass. There are two types:
1) Regional trains. There is no pre-booking on these trains, and no price advantage to pre-buying. Just buy tickets from the ticket machines on the day.
2) Express trains. On these trains you pre-book. The earlier you book the cheaper, but you can still buy full-price tickets on the day.

Now got to http://www.trenitalia.com/ and look up some sample times and prices for your journeys. Important: When you use the site, you need to know the name of the station (or town) you are travelling to and from "Dolomites" or "Cinque Terra" will not work. They will not have trains for next September posted yet, so choose a random date in about 1 months time.

For a very good and full briefing on all things to do with train travel in Europe, go to The man in seat 61. This is an excellent independent information site.

About your itinery: A car is a good idea for lake Como, as it is an area suited to touring (and very beautiful). I would return the car in Como town, and get a Regional train into Milan and change trains for Cinque Terre. Avoids fighting Milan traffic.

I would repeat the golden rule "at least 2 nights in every place". Each change of pllace takes ½ day. One night stays give you no time to appreciate a place.

Use
www.trenitalia.com

You can also purchase tickets ahead online. Discounted (Economy and Super Economy) tickets on Freccia (high speed) trains go on sale 120 days prior to travel day. The full price is called "Base". If you buy discounted tickets you save money, but you lose flexibility because they are not refundable or changeable. So if you pre-purchase make sure you are certain about your travel plans, because if you miss the train, you lose your money.

I don't know where you land, but if you land in Milan (the largest airport in Italy after Rome, and generally with the cheapest fares from North America) you could use this sequence of locations:

Milan > Lake Como (Varenna) > Verona > Dolomites (I would pick up a rental car in Verona and return it in Venice after roaming the Dolomites) > Venice > Florence > Cinque Terre > Milan > Home

Assisi and Siena can be done as day trips from Florence, but if you want to stay a few nights you can. Assisi can be reached via train from Florence while Siena can be reached via bus or train from Florence. If you don't do Assisi and Siena as day trips and prefer to stay a few days, you might consider renting a car after leaving Florence, visit Tuscany and Umbria, including Siena and Assisi, then return the car in La Spezia, near the Cinque Terre. You don't need a car at the Cinque Terre.

For purchasing discounted tickets ahead of time, I would consider only the Venice to Florence leg. All others are mostly on regional trains, that offer no discounts, and regional tickets are best purchased at the station when you leave (or the day before).

Trenitalia, a.k.a Ferrovie dello Stato Italiane is the Italian national railway service and operates nearly all trains, whether fast, medium, or slow, so there should be no need to look at any competing service and no need to drive these routes. None of your daily rides are very long, so train tickets will be pretty cheap to buy as you go; see standard ticket prices on the map at http://www.ricksteves.com/travel-tips/transportation/trains/italy-rail-passes.

For another link to train schedules that are easy to print, see How to Look Up Train Schedules Online, but note that it does not reflect the Milan-Varenna route.

Thank you all for your comments - they help a lot!

IMHO, most of what you are going to experience is the inside of a train compartment. Checking out of a hotel, getting to the train station and traveling to a new place, finding you hotel in a strange city, and checking in all take time. Subtract at least 1/2 day at each destination and you will see your time in each place is reduced. If it were me, I would drop two or three destinations and spend more time at each location.

Sometimes less is more. Your itinerary, in my estimation, is like a marathon at a dead run.

Buon viaggio,

A BIG amen to the above suggestion to reduce the number of moves.