Bus/train from Arles to Amsterdam

It's all possible but I think you should decide if you like the number of train connections on each leg, when they can't follow the same route that the crow flies. Looking Up Train Schedules and Routes Online gives you the Deutsche Bahn train schedule link and tips for using it.

Marseille to Arles and Arles to Avignon are fine.

There's something odd about the data I'm seeing for L'Isle-sur-la-Sorgue. I can't remember whether I took a bus or the train from Avignon; it seems there's supposed to be a train but it's not showing up on the schedules. In any event, you can certainly get from Arles to L'Isle by going through Avignon and possibly by a different route as well. The trip will probably be all-bus or a mixture of train and bus. Bus schedules in that area are date-sensitive (time of year and probably also day of week), so check carefully. Your options may be a lot more limited if you're not traveling during high season.

Arles to Annecy (via Lyon) also works, but pay attention to fares. Some of the routings cut through Switzerland, which I suspect will drive up the cost.

Annecy to Strasbourg (via Lyon, possibly) also works, and Strasbourg to Trier, Trier to Bruges, and Bruges to Amsterdam. On that last one you'll have a choice to take the Thalys (more expensive and somewhat faster) on the last leg or not.

You can play around with the schedules yourself (though perhaps not for your travel dates yet) on the Deutsche Bahn website. For fares, you can used SNCF. As you begin to pin things down, don't forget that it's important to check schedules for the right day of the week as the information becomes available.

Some of those travel legs look like they'll take 5 or 6 hours, which is going to cut into your sightseeing time and may mean you'll want more time at some destinations than you may be anticipating. As a result, I think as you fiddle with the schedules you may find that you don't have time to make as many stops as you're planning, in which case you might want to consider a budget-airline flight along the way--perhaps Strasbourg to Amsterdam, for example, if you need to skip Trier and Bruges. The airline HOP! has three non-stops on the random May date I checked.

This site will tell you all you need to know about European train travel:>https://www.seat61.com/France.htm

Thank you so much for the help!! I am going to your RR websites and getting good information. I think you may be right that I should fly from Strasbourg to Amsterdam....perhaps spending more time in the south and in Annecy. I will keep researching!!