The canoe worked out fine, but was larger than necessary from the headwaters down to Bemidji. Bemidji State University’s Outdoor Program Center rents smaller (pre-scratched) canoes that would have been more appropriate for that first stretch.
I agree that it might well be a good idea to hire one of these smaller canoes and then up-grade in Minneapolis. I've been jotting down a list of things that would need to be done before we set off and most of them can be done from a distance. This seems the ideal way to avoid having to do a lot of preparation in situ.
Incidentally, I followed the links you posted and was looking at some photos of the river in its very early stages - it made me very excited! (Have ordered a big map of Minnesota for my wall at work...)