1. Just take I-5 thru Seattle between 10-2 and you'll save a lot of time and money. It's not that bad. I especially wouldn't take the loop around to the east as it's WAY out of your way.
2. Ferries cost money and depending on the size of your rig, could cost you almost $100 a trip. I wouldn't worry about getting on and off either.
3. Port Townsend ferry now has the reservation system. You gotta call in advance. Also, the San Juan ferries do also and I have heard some real horror stories about that deal.