If you are interested in architecture the Frank Lloyd Wright Foundation owns Taliesin, the house Frank built for himself near Spring Green (and House on the Rock, see above) it is open for tours and there are other FLW buildings in WI: http://franklloydwrightsites.com/wisconsin/index.html
and the State Capital in Madison is pretty impressive.
American Players Theater, also near Spring Green, will still be presenting plays on October weekends, in both the Touchstone Theater (indoors intimate) and Up The Hill (outdoors large) http://americanplayers.org/
They close during the winter.
The Sister Bay Fall Festival in Door County (see above) is October 16-18 this year. It usually coincides with good fall color.
The State Historical Society owns Villa Louis, a lumber baron's mansion in Prairie du Chien, near Wyalusing State Park (see above). It is open for tours. The Historical Society owns several other "living history" museums around the state. Another is Circus World Museum in Baraboo, near the International Crane Foundation and Devils Lake State Park (see above). Circus World offers a big top tent show, circus memorabilia, and historic circus wagons. Baraboo was the winter home of the Ringling Bros., Barnum, and Bailey circus.
The Wollersheim Winery near Sauk City, south of Baraboo, offers tours and tastings and arguably the best wine made in Wisconsin. But Wisconsin is a beer state so don't get too excited. But it is a nice tour and their Prairie Fume is a moderately dry, pleasant, and reliable white.
Also near Baraboo is the Mid-continent Rail Road Museum in North Freedom--steam train rides and railroad history.
If you do go the Sauk City you should not miss Dr. Evermore's Forevertron http://www.travelwisconsin.com/museums-galleries/dr-evermors-forevertron-198057
The Kohler Company factory tour (plumbing fixtures) in Kohler is interesting and the American Club (another Kohler business) in the former Kohler workers' dorm has at least three restaurants priced from affordable to astronomical. Kohler-Andrea State Park on Lake Michigan, south of Sheboygan, has a beautiful beach to walk and very nice sites. It is close to Kohler.
Allen Edmonds does not offer a factory tour but you can observe the factory floor from their discount store in Port Washington. Excellent shoes made from scratch in USA.
Wisconsin has many, many bike trails, too many micro breweries to mention, and a lot of artisanal cheese see Wisconsin Online: http://www.wisconline.com/
Here is the site for Wisconsin Parks and bike trails, but there are many city and county parks and trails not shown: http://dnr.wi.gov/topic/parks/findapark.html
I agree that Bayfield and the Apostle Islands are very nice but they will be hoping for snow by October. You should come back and tour north of WI highway 8, including the Michigan Upper Peninsula (UP) in September.