Itinerary help

Your itinerary will take you through some breathtaking scenery, and you're traveling slowly.
If you've not made your flight arrangements, why don't you fly home from Florence--open jaw? Backtracking to your arrival city is often very expensive.
I would suggest picking up a rental car in Florence if you want to see the hilltowns south of there. There's a Hertz location about 2 miles and a cab ride from the train station--away from the ZTL. You could turn the car in at the airport. Tuscany has hundreds and hundreds of agriturismos to stay in for very fair prices.

Rather than subjecting yourself to two hotel check-ins in Milan, I'd consider going straight to Lake Como on the day you arrive. It's a short trip from Milan, and I assume there would be no problem buying last-minute train tickets when you arrive.

I like that you're giving yourself time to see the places you're visiting, but four days seems like quite a lot for the Cinque Terre, which are perhaps not the best base from which to make day-trips.

Bergamo's a very atmospheric hill town about an hour by train from Milan, should you decide you have time for a day-trip.

I just looked up Bergamo and it looks beautiful so that may have to be added. Would public transportation work well with this plan. I figured the rental car might be our only option for getting around Tuscany.

So far, it sounds like a train/bus trip except for Tuscany, where it would be great to have a car. You mentioned having already visited some of the popular hill towns, and those are likely to be the ones easiest to reach by public transportation. Sort of by definition you're now left with the equally charming places that are not so easy to reach. It's when I'm visiting places like Tuscany that I'm a bit frustrated by my inability to deal with a manual-transmission car.

Gmeseck,
When will your trip take place?

Have you booked your flights already?

If not, I'd suggest traveling to your desired destinations in Italy, before heading to Switzerland & perhaps flying home from Geneva (or Zurich), to avoid back tracking back to Milan.

Do consider staying in Varenna, on Lake Como, as it's on easy train (one hour) train ride from Milan.
Which village are you considering in CInque Terre?

As I said, I am in the very early stages of planning. I have just ordered my Rick Steve's books but here is what I have been thinking. I would like to go the first part of September 2017. No air booked yet of course. I was looking at renting apartments in most of the locations and agratourisimo (sp?) in Tuscany. I was looking at Varenna in Lake Como and Gimmelwald or Murren in Switzerland. In Cinque Terre the three places I was looking at are CornigliaLerici or Portovenere but I really don't know which is best there, suggestions? I had chosen Milan for flying in and out of simply because it's a larger city very close by train to the places I wanted to see and because we had never been there.

As David said, you can consider flying into and out of different cities to avoid backtracking. If the price/schedule are right, you may end up deciding on a round-trip to Milan, but you don't necessarily have to do that.

To avoid the possibility of confusion down the road, Lerici and Portovenere are near the Cinque Terre (to the south) but not part of the Cinque Terre.

Murren is a better choice than Gimmelwald. You can walk down to Gimmelwald from Murren and see it, but there is NOTHING there. It is a cute farm village but Murren is more suited to most of us, Rick Steves' recommendation aside.

Corniglia, Lerici or PortoVenere...none are well connected by train in Liguria. In Corniglia one must either wait for the shuttle or be willing to walk up-and-or-down a huge mass of stairs to the train. Neither PV nor Lerici is served by the trains, only by buses and ferries. I think staying in a town that is served by the trains makes the Cinque Terre more fun. One of the other 4 villages or a bit north in one of the other small Ligurian Rivera towns.

Four nights in Cinque Terre might be one night too many, unless you are into hiking in a big way. We spent a couple of nights there two years ago, and that was enough for us. Another night would have been OK, but four nights seems a lot.

Have a good look at what is on offer there.

Thank you all so much especially for advice on Cinque Terre! Where would you recommend as the best place to stay there?

Where would you recommend as the best place to stay there?

This has been discussed to death on this Forum. If you search above and read some thread from the last 6 months, you will find many many opinions and options. Of course Rick Steves' guide is a great source as well. Do you have it?

I have ordered Rick Steve's guides. I rush to the mailbox ever day. It can't be long now.