I'd try to not miss New Glarus (south of Madison). That's probably the best in Wisconsin.
One thing I'd suggest is going up I39/51. There are a couple of breweries along the way, one in Plover. It's really good, and people like it.
http://www.osobrewing.com/Home.php
Point Brewing is popular as well (in Steven's Point). They have a tour, I believe. There are a couple in Wausau, but are newer and I haven't been there (except for Hereford and Hops, which is decent). There is Central Waters in Marshfield, but I don't care for their beers much. Others do, so it may just be me. Legends (Green Bay and Appleton) is terrible, but the food is ok (like an Applebee's type).
I just can't think of anything at all along HWY 41. You could go up I39, and then cut over on 29 to go to Green Bay.