Do you have this web site? While it says Les Plus Beaux Villages, it is not the official site. It lists some of the official ones, but also other villages. I use it when researching our trips. It is in French but google translate helps.
You probably already have France voyage which gives regional foods and tourism ideas, but I will add it.
Basically, what we do is work out the route and then look up towns, villages and natural features on the way.
Good luck with your planning. Sounds an interesting trip. We are planning for 2020, but will probably be Burgundy , south and south west again- our favourite regions.
Since sending my post above, have researched and found a route and small towns along the way which look interesting.
Le Hohwald - Luneville - Saint Nicolas de Port - Pont a Mousson - Metz
We try to avoid tolls and motorways and that way always seem to come across many unexplored areas.
We use Via Michelin Route Planner and although we find that the quoted times are not always correct, it does give alternate routes other than toll and motorways.
I wlll look at the sites you have given. We are very much looking forward to this holiday. I think the Jura will be amazing plus other areas we have not travelled.
Thank you again for your feedback.
We travel mostly on departmental roads - much more interesting. We did not pay any tolls last trip in 2018, but did travel briefly a few times on free autoroutes. We also use viamichelin and we like to allow time to stop because you never know what is around the corner.