Best route in September

Assuming your cruise ends in Paris, based on real transportation options to where you want to go:
Here is an itinerary:
Take the Train from Paris to Arles. Stay a week. (2nd week of your trip)
Then take train Arles to Marseilles Airport fly to Rome (3rd week of your trip)
This is the only direct flight close by.
Stay in Rome and then go to Florence (all one week).
Florence to Interlaken (4th week of your trip)
You can either take 7 hour train ride to Interlaken from Florence or fly to Geneva or Zurich and then take a train to Interlaken.
Stay in Interlaken 3 or 4 days.

If you really want to go to Saleema, Portugal based on this order and transportation availability you can take a train to Basel and fly from there to Faro and then rent a car or take a train to Saleema.

Curious why you're only giving Amsterdam one night but small Brugges two. Perhaps you have already visited wonderful dynamic Amsterdam?
Interlaken: go into the mountains instead. It is set between two lakes but in Switzerland you want to be in the mountains.Look at Grindelwald. It is so much charming than Interlaken; you will have the most beautiful mountains right outside your windows. It is well connected by trains.
Tuscany: I recommend that you rent a car for this part of your trip or you will miss so much of what makes Tuscany so special. I have never used trains in Tuscany except to leave Florence for Venice. I do not know which towns are connected by train lines. Perhaps Orvieto in Umbria would work. Look at Siena too, in Tuscany.
Provence: a week there is good and we enjoyed Arles.
Portugal- are you allowing some time in Lisbon? We spent ten days there and took day trips by train.
I am sure you realize that each time you travel to another country/ area , you loose valuable time.
As far as expenses, Portugal will be the most economical and Switzerland the most expensive.

Jazz + Travels and Suki,
Thanks for your replies and we'll look at flying out of Marseilles. Suki - our trip this coming year is to capture some of the areas we missed in 2014 plus explore a couple regions in France that have a lot of interesting history to us, as well as in Portugal. Your advice is well put and follows what we did previously.

I have been to the Algarve, but not recently and never to Salema, but other posters here have had rather negative things to say about Salema in comparison to other options on the coast. If you don't receive comments on Salema on this thread, I suggest reviewing the Portugal forum for posts referencing Salema.

Realistically for enjoyment sake, I would be forsaking Portugal on this trip.

7 nts - Amsterdam, Bruges, Paris
7 nts - River boat cruise to Normandy
5 nts - Provence region of France
5 nts - Berner Oberland in Switzerland
7 nts - Tuscany & Rome

David has a good plan. It seems a long and expensive option to go to Portugal. It is an outlier.

I'm also wondering why you are planning to spend your first night in Amsterdam. You'll be sleep-deprived and jetlagged after the trans-Atlantic flight, so you won't enjoy A'dam very much on arrival day and then you're off to Belgium. Either spend a couple days in A'dam or take the train to Bruges (via Antwerp or Brussels). Or just fly into Brussels.

Have you been to Paris? How many full days do you want to spend there?

How are you going to get to/from Salema? I looked at rome2rio.com and Arles > Salema takes 11 to 14 hours with a flight - almost twice as long without flying. Though if you have a car in Arles, you could drive to the Marseilles airport, then rent a car in Faro and drive to Salema. That would save some time, though you still ahve to factor in the time to pick up and return the cars and at least an hour's drive from Arles and another hour to Salema. Arles > Interlaken (if you drop Portugal) is 8 hours by train (that's the only direct route). Interlaken > Florence is about 6 hours on the train. If you are not going to rent a car in Portugal or Switzerland, your journeys are going to be long with several transfers.

Rome is not a day trip from Tuscany. It's a fairly expensive 1.5 hour ride on the fast train from Florence, not counting the time to/from the train stations. And it's worth a lot more than a day trip. Florence is the best base to day trip in Tuscany, but you'll use buses as much or more than the train.

As you've already taken at least one European trip, you know what travel tempo suits you. Just remember that to get 4 days in a destination you need 5 nights. It's easier to count nights, since you don't "double count." A day between Arles and Salema is not a day in Arles AND a day in Salema, it is not a day in Arles OR a day in Salema, it is a day of travel.