I have not taken the Kingston ferry on a bike tour, but I did take the Bainbridge ferry on a trip to Port Townsend. Here is the route we took:
Seattle to Port Townsend
The hood canal bridge was fine and I did not feel unsafe. There is a huge shoulder on the bridge. I think, many moons ago, it was not so good, but it is fine now.
Here is a view from Google Street View.
The return route we crossed over from Port Townsend to Whidbey. The one thing I would have changed with this route was the route from Mukilteo to the Interurban trail. The route we took was not good.
Port Townsend to Seattle
I realize the routes I included above are not exactly what you are looking for, but maybe they will help.