I agree with others have said, particularly the ride north/ferry south suggestion, as the distances will wear you out if you plan on covering a lot of ground in only 2/3 weeks. Driving north is no sweat as you're pumped to get there, but on my way home I was happy to see the ferry.
FYI, if you camp, tents are NOT allowed under the solaruim, so you are exposed to the elements. Fortunately, I had sunshine for my whole trip from Haines to Bellingham this August. It is wise to bring your own tie downs for the bike, as they had run out by the time I boarded. No worries tho' as the trip is all in the Inside Passage, hardly entering open water.
Bring some food as the boat grub is pretty bad and overpriced. The stop offs are great, particularly Sitka. They show movies and give wildlife/history talks and have a bar on board, so the time does not lag.
I also ferried from Whittier to Valdez (about 6 hours) which was great. Both ferry rides prevented me from having to retrace many steps on my trip.
You gotta camp...cabins are for fairies
Weather, as always in Alaska, makes a big difference...