All the destinations listed on the recommended itinerary are nice destinations for a first visit. I would recommend you buy a Waggoner's Guide or the "Gunkholing in the San Juan Islands" book (by Bailey and Nyberg) if you want some local color and history of the places. These will give you good ideas for alternate destinations and places to anchor for lunch.
To use yacht clubs in the area, your club would have to have reciprocal privileges. Waggoner's lists the yacht clubs and yacht club outstations. Check your yacht club listing for clubs with reciprocal privileges. In any case, most of the marinas in the islands are well-kept and well run.
For your first day (Anacortes to Lopez Island) I would recommend you stay at Spencer Spit State Park, either on a mooring buoy or at anchor. The north side of the spit is exposed to ferry wakes, but that isn't too big a deal. The park and beach make for a great on-shore excursion.
On your way to Friday Harbor, anchor in Indian Bay (Shaw Island) for lunch, and then continue to FH, which is the hub of the islands, with a well-maintained but busy marina.
Roche Harbor is very protected and pretty, good for anchoring or staying in the marina. The upscale resort is very quaint. The jet set keeps their boats here during the summer.
Reid Harbor (Stuart Island) is a state park, and a very nice quiet anchorage. There are hiking trails. This is one of my favorite spots. It is a short motor or pleasant day sail from Roche.
I've only anchored at Sucia Island, but most people consider it a must-see.
Rosario Resort is only partially open this season, and both the mansion and the marina will be closed after Labor Day according to thier site (
http://www.rosarioresort.com/), so you'll probably want to plan another stop or just stay another day enjoying Sucia.
Enjoy your days in the islands!
