Many churches will be having concerts beginning with Ash Wed. & Lent and then again at Easter. Check with any churches in the cities you will be going to and see if they have concerts. I have a couple of them here for Frankfurt. Hopefully, if you hear of any other cities, you will add them to the list.
Kaiserdom (this organ has over 8000 pipes!)I know the website is in German, but the dates, the composer, the times and the prices are fairly self-explanatory. I do think hearing Handels "Messiah" might be well worth the price there. http://www.domkonzerte.de/domorgel.htm
Alt Nikolai - though this is quite a small church, its' simple, Gothic loveliness works well for small concerts and the acoustics are wonderful here. Switch over to the kalendar for concert dates.
http://www.paulsgemeinde.de/english/index.html