I'm German and I'm living in the north of Baden-Württemberg. (The sources of the Danube are in the south)
I always had the impression that Britain is more handycap-friendly than Germany. So, there might be some issues.
Unfortunately I'm not an expert on wheelchair life and travel but I know Germany quite well.
First a question: How do you plan to move inside buildings? Will you take a small wheelchair with you?
For the transport: Here is a link to the wheelchair pages of Deutsche Bahn.
From my personal observations, I would say it can be quite a hassle to get on trains. Sometimes the staff of the bahn has to get a ramp to get you on the train but it seems to be always possible. It seems to be important to state in advance that you need to get on the train by wheelchair.
There is a convient train line through the Black Forrest from Karlsruhe to Konstanz (on Lake Constance) that stops in Donaueschingen. When I toured the Danube with my son, we got off the train in St. Georgen, giving us 20km along the Brigach river on a convinient Radweg mostly downhill to Donaueschingen.
Have a look at http://www.bahn.de
For accomodation, the trick is to google "barrierefrei" (barrier free). E.g. I found a bit of information for the Alb-Donaukreis
(a Landkreis (county) at the Danube). They tag wheelchair accessible accomodation
, but you can't search it. So you have to click on every item to find something. This is just an example. There must be better ways....
If you have any question or if I can help you with translating, feel free to ask here or give me a private message.
Have fun at the Danube!