Champagne/Alsace/Burgundy area recommendations

We stayed in a gite in Ribeuville in the Alsace - great location for the Wine Road and the Vosges. Lots of stores and restaurants in the area, and we loved the location. When we stayed in Burgundy, we stayed in a gite in a small village, Monthelie, just south of Beaune. It's very close to a number of other villages, lots of walking and biking trails, nice restaurants, and very near to Beaune.

It's a big tour you are planning ... !
I am personally living in Burgundy so I can only give you insights on that particular region.
Coming from Alsace you could start with Dijon which is worth a visit as the historic capital of the Dukes of Burgundy. The small town of Beaune and its area are well-known for the wine industry and the Hotel-Dieu, a medieval hospital. Definitely a must-see. In the surroundings are numerous Domaines and Chateaux to visit if it is among your interests.
Driving south, the area of Chalon ( my hometown actually ) gives its name to the Cote Chalonnaise, one of the wine appellations in Burgundy : plenty of quaint villages, lots of medieval buildings or monuments including the abbey in Cluny and the church in Tournus. Castles, fortresses and Romanesque churches abound all around as the whole Burgundy is rich in medieval remains.
Depending on your route there are two top-hill villages that are absolutely worth a visit : 1) the village of Oingt in the Beaujolais region about 40 km north-west of Lyon. 2) the village of Pérouges about 50 km north-east of Lyon.
These are only a few suggestions. For anything specific re accommodation it would be good to know what you are looking for.

For accommodation in Burgundy I would very happily recommend the Carpe Diem Guesthouse in Massangis. We spent several nights touring with our car. Our room was huge and beautifully decorated ( the rooms are named; I only recall that our room was red...if you look at pictures). The bathroom was modern, large and sparkling clean. Breakfasts at the dining table with other guests was delightful. It is an old farmhouse in a tiny village with lovely garden areas. Money-wise, you will be hard pressed to find better value for a reasonable price. I worried about how remote it seemed as we drove in, but we easily accessed everything we wanted to see. Patrick and Eric were wonderful hosts. We used their Michelin guide to plan each day's drive as it offered several different suggested routes...very helpful. Among others, we visited Auxerres, Autun, Vezelay, Fontenay abbey, and Chablis. We did not partake of their dinners but other guests who did were all pleased. . Several restuarants are in the nearby and likewise tiny town of Noyers...we had nice meals there and in the area. I found them on Tripadvisor. The reviews are to be believed. And the owners respond frequently to posts there, something that I like to see. The combination of lovely accommodations, relaxing environment and gracious hosts made this a memorable visit to a beautiful area.

Thank you for your help and upon further reflection I agree it is too much. I think we will skip the western portion this time and take the train from Paris to Strasbourg, pick up the car there and head South zig zagging.

During a trip to Lyon a few years ago we visited Perouges and Vienne. Both worth a visit.