howdy -
I've taken the SS Badger from Wis back to Mich. A few years ago. There was a bike rack on the ferry where you wheel down the ramp, like the kind at the library. You should take some bungee cords or other straps to keep it vertical. I didn't have anything and I was preoccupied with a tick I had just pulled off my arm. After the boat ride, my bike was laying down. I was thankful my front wheel didn't get all out of whack. Kudos to Velocity Cliffhangers!

About 2 years ago I biked the coast (west coast or east bank? you decide) from New Buffalo up to near Sleeping Bear Dunes. I decided to go mostly pavement. It kind of sucked, due to fast traffic. I thought I'd get more of a view. But that's prime housing property. So, no. Mostly I was following M22. The highways changed names a couple time: Blue (death) Start highway; Red (poison) Arrow (of death) Highway. I'm sure there was another death highway in there. (tangent: I also biked up the east coast along the thumb - then I got a water view most of the way to the tip of the thumb!)

There are some rail trails, and it's getting better. I'd just check out Google maps for the rail trails and click that bike path button thingy.
There's also this:
https://www.michiganoffroadexpedition.com/
- if you're of the more adventurous.
Also - depending what time of year you go, the SS Badger does night crossings.I think from Luddington you can get a 9PM ferry and be back in Manitouc at 1AM or something. Maybe midnight. . . somebody google that for me.

I'm thinking about using the high speed ferry, the one that goes to Milwaukee, then maybe touring Door County. Not sure yet.
Safe Travels.