we will likely be taking the train into France to Colmar/Beaune So we
will be passing through that western edge of Bavaria if there is
anything that's a must see on the way out, we could definitely spend a
day or two there
OK, that's helpful information.
There are many places in Germany including those you mentioned previously that you might visit both before and after leaving Bavaria.
For general reference here's a map of the German states (Länder)
You could probably spend 1-2 weeks in Baden-Württemberg too. But let's assume maybe 1-3 days, as you have indicated. Below is a strategy to create an intelligent train itinerary between Bavaria and Colmar but still see a place or two on the way.
German Railways (DB) will offer a variety of routes to Colmar depending on where you are when you leave Bavaria. Some via Switzerland, Austria, and France, some just via Germany and France (which is what you are looking for, right?) Here's the itinerary search page:
Let's say you're in Füssen (easily reached from Munich by train) at the end of a dead-end railway in the German Alps (or in Garmisch just to the east - it's also easily reached from Munich and on a railway to Innsbruck.) Let's say you have Mercedes on your mind and Stuttgart is a must-do. To find your routing, your "from" is Füssen, your "to" is Colmar... you click on "add intermediate stops" under "stopovers" in order to enter Stuttgart Hbf in the Via 1 box (no stopover time is required just to get your routing.) Once that is done, your resulting itineraries will ALL make a stop in Stuttgart.
Now, click on "show details" and find "map view" near the end. Click that on to see the routing and the stops (big circles.)
You mentioned the Black Forest...Let's say you also want 1-2 days there. But oh... the above routing sends you directly to Strasbourg in France and bypasses the Black Forest :( No problem. Just click on "change" near the top of the page and enter a second stopover in the Black Forest town that interests you. Then you'll have a routing to that town as well as a routing from that town to Colmar.
Try Gengenbach. It's an extra-nice old walled town with good access to the Black Forest near Offenburg and Strasbourg. Enter it as a Via 2 stopover. Then go to map view and you can see the routing for your whole trip.
Besides Gengenbach's own appeal, Gengenbach lies on the scenic Black Forest Railway and provides access to other Black Forest towns at higher elevation (including Schiltach, Triberg, Villingen-Schwenningen, Donaueschingen, Haslach, and Gutach, home of the Vogtsbauernhof open-air museum.) But other towns can be good too. Note that Gengenbach and other KONUS towns hand out free guest cards good for free train travel around the Black Forest.
Now, once you have your destinations towns and routing you can plan your time in these places and figure out later how you will ticket your trips day by day (or figure out what sort of multi-day pass you will buy.)