Tagster, sounds like fun. What kind of boat do you have?
I've known a couple of people that have taken pretty much the same trip. There are two schools of thought. One is to head offshore 60-120 miles all the way down to SF. The other is to harbor hop. Not necessarily an easy proposition on much of the Washington/Oregon coasts, as deeper drafts can make some bar crossings difficult (not to mention the conditions themselves).
If you don't already have a guidebook, take a look at Exploring the Pacific Coast—San Diego to Seattle, by Don Douglass and Réanne Hemingway Douglass
. They have a good reputation, and I know of no other complete guides to the Pacific Coast.
Exploring the Pacific Coast
When do you plan on cutting the dock lines?