switch07,
I have done parts of this trip on several overnight trips before. Here is my .02 for a loop.
Day 1 is Moose Lake to Grand Marais area via Cloquet, Fish Lake and the North Shore Trail (not around/thru Duluth). I say area because you could stay on top of the hill at one of several places (devil track resort, hungry jack lodge, trail center lodge) or down in town.
Day 2 starts by heading to the end of the gunflint, and then back to the NSST and south to the Tomahawk Trail to Ely. A ride on the Tomahawk is not complete without a stop at the Trestle Inn, about 10 miles off the NSST. If its lunchtime, the Trainwreck, or Trainwreck with casualties, is awesome! Then it is on to Ely and to the casino in Tower on Lake Vermillion. If your up for it, you can take the lake or land trails to the west end of the lake to The Landing. Good food and an outside ice bar in years past.
Day 3 is Tower to Baudette, via Crane lake and the land trails up to Ash River and on to International Falls. All of Voyageurs Park has a 40mph speed limit, and 25 on portages, which is why i prefer to ride the land trails. Plus this year to date there has been a decent amount of slush on the lakes. Then over to Baudette. There are many places to stay there, but, it is a huge ice fishing destination so it may be wise to try to find a room in advance.
Day 4 is Baudette to Roseau via the Northwest Angle. Make a stop at Oak island, then head up to Youngs Bay for a late breakfast. Ride the land trails back down to Warroad however you want, but think about stopping at "The Patch" for lunch. Then over to Roseau. Depending on the time, you could either try get a tour of the Poo plant that afternoon or the morning of
Day 5. Roseau to Bemidji via the north and east shore of Upper Red Lake. Shorter day with options for side trips.
Day 6 is Bemidji back to Moose Lake, again the Soo corridor can make for quicker travel but there are other loops you can explore off of it.
As you can see I am from Cloquet. On your way north you will pass about a half mile from my house. If you look on the MN map there is a small gap when you go north of Cloquet towards Fish lake, just before highway 53 at Grand Lake. I can draw you a map for the route thru this gap. It is only about 3-4 miles and is easy and legal and well used.
I'm envious no matter what routes you decide to take. Safe travels!