The day I crossed lake Michigan we had high winds and fairly rough seas. However the Lake Express ferry has plenty of tie down points on the parking deck, so you should have no problems. I recommend 4 tie downs. My bike made it across without a hitch. Beats the heck out of traffic on I-94!
Anyway, I may re-paint my bike next year to the BMW stock red color, and get the system case lids painted to match. However a lot depends on how gracious my wife is with the checkbook...
Best of luck!