Re: San Juans; advice & suggestions
Ray about covered it above. Cap Sante (Port of Anacortes) Marina has free parking for cars and trucks but no trailers and I'm not sure what the fee is at the lot by Safeway that allows trailers. Washington Park is probably your best bet, and it's a few miles closer to the islands.
Perfect timing for your trip, the crowds will be gone and you'll probably have your pick of mooring balls at the state parks, and September typically has great weather.
For your first anchorage you can take your pick; James Island is just on the other side of Rosario St., Spencer Spit is always great and it's just a few miles further. If you want to head north for Sucia but want to break it up there is a park on the east side of Cypress Is. that is nice, or like Ray said, Doe Island on Orcas.
As far as "don't miss" places I would say Sucia Is., Patos Is., Stuart Is., , Roche Hbr., Jones Is., Friday Hbr, Fisherman's Bay on Lopez Is. (Lopez Village farmers market on Sat.?), Spencer Spit on Lopez. That's a good start anyway and in that order makes for easy days travel (watch the currents).
SV Laurie Anne
1988 Brewer 40 Pilothouse