Best way to see Alaska is by vehicle and without any plans. From Auke Bay, take the ferry to Skagway and spend a day. Drive FAST through Canada (nothing to see there), and go to Fairbanks, then Anchorage. On the way from town to town, stop, as mentioned above, at all the parks and such. The animals are usually not a hazard in the daytime, but at night they can be an issue.
Auke Bay is Juneau - Take a few days and hike some of our trails - Mt. Roberts. East and West Glacier, and so on. See the glacier(s) - lots of penguins
See the Alaskan Brewery - lots of good beer for tasting.