Thanks again for all of your input. Our (almost) final itinerary is much saner than the original! All comments, suggestions, observations, etc. are very much appreciated. We are now less than a month away from the trip!

Here is the revised itinerary:
Day 1 -- fly to Anchorage; drive to Girdwood
Day 2 -- Girdwood & 26 Glacier Cruise
Day 3 -- Travel to Seward; Exit Glacier; Sea Life Center
Day 4 -- Kenai boat trip (full day); drive to Anchorage
Day 5 -- Anchorage; fly to Haines via Juneau
Day 6 -- Haines; late boat to Skagway
Day 7 -- Skagway
Day 8 -- boat to Juneau; downtown Juneau
Day 9 -- Mendenhall and whale watching boat trip
Day 10 -- Tracy Arm boat trip (all day)
Day 11 -- Juneau (activities undecided)
Day 12 -- ferry to Sitka
Day 13 -- Sitka
Day 14 -- Sitka
Day 15 -- return flight from Sitka