erps has been cruising up here longer, but my favorite guide is
Amazon.com: Gunkholing in the San Juan Islands: Jo Bailey, Carl Nyberg: Books
Written by a couple of folks who have been cruising the area for many decades. They tell great stories, and have a true love of the area.
A bit outdated, though. That shouldn't matter much.
The Wagonner Cruising guide is updated every year, and is more "marina oriented"
The Waggoner Cruising Guide, Annual Guide to Northwest Boating from Weatherly Press
The Maptech chart guide for the San Juans works well for me:
http://www.maptech.com/search/prodse...DF/WPB1510.pdf
Since you are going to be slow (sorry) and 3 knot currents are real common, I'd recommend the following current current atlas: (don't forget to also purchase Washburn's 2009 Tables, so that you can use the atlas)
"http://www.shearwaterkayaks.com/shop/chartsnav.html]"
I'm looking forward to my 4th summer of cruising the San Juans. I've managed quite well so far with the above publications, a hand-held GPS, compass, and a bit of common sense. I expect that you can too.
Make sure you let us know when you will be up there, and we'll watch for you!
Best wishes,
David