I know you have mostly settled on a route down to the California border, but I will throw out a couple of suggestions anyway.
My wife and I rode the Pacific Coast Route, and had many trips in the Puget Sound, San Juan Islands, gulf Islands, and Vancouver Island areas.
We started the PCR heading north from Vancouver, BC to Lund and then came back Canadian Hwy 101 to Powell River to take a ferry across to Vancouver Island. We then headed south to Victoria, BC. It is a beautiful city. Then take the ferry across to Port Angeles, Washington which puts you back on route. This may require a few more days, but it is well worth it.
The true PCR starts in Lund, BC
Heading into Victoria
I would also suggest taking your time going through the Redwood forests in northern California. The "Avenue of the Giants road" is a great part of the route. There is a lot of info/maps on the web about the area.
These are the small trees, and not much light gets to the forest floor.

Have a great trip, and don't forget your rain gear!