If I were you I would make Bucknuckles Bar and Grill my destination... coming from the south as you are, take 88 north just after fountain city. Go through cream and then The restaurant is on the left just after T.
On the way back to the River Rd just take T to N to S to 37 (they have a saying at the bar that makes directions easy). Then you can go acoss the river at Nelson/Wabasha.
Regardlss, you should stop at the creamery in Alma for ice cream.
If you are able to go even further north than Nelson/Wabasha that is a really nice ride around Lake Pepin. The WI side is very slow through small towns but they are cute and have fantastic little bar/restaurant stops. The Minnesota side is much quicker, but if you go in the afternoon the sun is across the river and the shade can get very cool by the water...
At a minimum I would think you can ride the WI side from Prairie du Chien up to the Winona crossing as it is only 100 miles.
Sometimes it is fun to criss cross the river as you are going along. But sometimes running one side all day gives ya a good feeling, especially going by the landscape from the other side of the river the next day.
There are soooooooo many little side roads along your route. You can take a small creek road to a ridge road back down to another valley road endlessly, and with the big river so close it is always easy to find the Great River Road again... it is downhill!!
I am having a hard time with the hotel bit, because there are AMAZING campsites on your route. I was watching Eagles and their youth all week from a campsite at Merrick State Park just north of Fountain City... some fun creek roads around there as well...
Ride Safe and Enjoy it.
"...there won't be any money. But when you die, on your death bed, you will receive total consciousness. So I got that going for me... which is nice."