Your plan sounds like a good one to me. You are wise to leave time to just poke along and leave time to do what ever turns up as you travel.
If you are looking for a place to sleep then the hotels around the Park entrance are your best bet. The princess McKinley Lodge is about an hour and a half from the park entrance. Have not stayed at the Princess Lodge located at the Park entrance for many years and to be honest it was not as nice as the other Princess Lodges. I have stayed at just about every other of the Princess Lodges and they are something special.
If your cruise stops in Skagway, I highly recommend renting a car and driving to Emerald Lake. There is also a train that it is available, but IMHO driving yourself is cheaper and gives you the ability to stop and take all the pictures that you want. The scenery along that road is some of the best in Alaska.
One other tip is to sit on the right hand side of the bus or train as you travel to Seward or Whittier. The first twenty miles, or so, is along Turnagainarm on your right with the side of a cliff on your left for much of the first part of your trip.