When I lived in MN, we would go to the mississippi river and have a great time fishing for small mouth and walleye. If you go up I-94 to the monticello area and fish north of there you will have good opportunities. I don't remember a lot of other fly-fishermen in MN so if you can spot some good rivers you will probably have it all to yourself. Most of the people that live in MN are on one of the many beautiful lakes. If you go Muskie fishing go up to Lake Mile Lacs. The fall fishing is unbelievable and the walley bite is great as well. Just be sure you dress for all different kinds of weather, it can change very quickly.
Enjoy your trip and make sure you post some pics when your back.