The best all around guide to Alaska, is "Exploring SE Alaska, by Don Douglass and Reanne Hemmingway Douglas. This is a very detailed guide. (They also put out a large scale chart for planning). For harbor details, Charlie's Charts of Alaska, give the best actual harbor detail.
Rather than Waggner's guide, consider Northwest Boat travel, which includes SE Alaska.
As for trailering--you are best going to Prince Rupert and parking there. You need to have a secure place to leave the truck and trailer in a locked compound. (The fellow I used, has a lot out by the fuel depot outside of town).
Marinas, are for the most part state or city owned. There is a large amount of turnover, and often there is hot slipping, since local boat's slips are assigned to visitors--or end ties are used.
Cities would be Ketchekan, Wrangell, Petersburg, Juneau, Sitka. There are also slips available at Hoona, Elfin cove, and many of the smaller villages, have floats, but generally they frown on some one tying up there for weeks.
Unless you are taking the truck and trailer on a ferry, I would not consider taking the rig to Alaska. You can drive on Prince of Whales Island, but that is fairly limiting--best to put in a Prince Rubert and boat the rest of the way.
If you are willing to pay postage, I would loan you my Douglas Guide, Charllie's charts and a 2009 NorthWest Boating. My Wagoneer and Milepost are a few years older, but for the most part still valid. I left a nunber of cruising guides with Paul Priest of Sequim for C Brats to use, covering the san Juans, Gulf Islands, and Vancouver Island to the Broughtons. Contact Paul to see about borrowing those books (about a dozen or so).