The timing for fall color should be good, it is usually over (leaves have fallen) by the first week in October.  We have some leaves starting to fall from our Basswoods now.
I plan to take Hwy#1 to Isabella/Tofte, then some backwoods DNR gravel roads over to the Sawbill area and Brule road.  Although gravel the back roads are good going, no ruts or soft spots.  There is a Superior Natl Forest recreation map with good road information available.  Sometimes the numbers are not displayed along the road well and you need to sort it out by also using the map and noting certain lakes, creeks, etc. you pass.  It should be a fairly well marked road as it is a popular place to go camping in the summer.
You may have to pick up your permit at Isabella station, it being the closest, altho you could also get it in Ely.  You can come up through Duluth and continue north on Hwy 61 to Hwy 1 at Finland, skipping Ely.