Sorry for the delay... it has been a busy week. I'm thinking two nights on San Juan Island and three nights on Orcas Island. I'm not familiar with Whidbey Island however I imagine two nights would be enough to see the highlights. Check with your innkeepers to see how busy they are during your time.... if your here during the shoulder seasons there is a good chance that reservations would not be necessary and you could easily add or subtract days at destinations depending on how you like it. Your innkeepers will definitely be able to provide you with the best exact itineraries as they will be informed about current events, latest restaurant reviews, park hours, and gallery exhibits. Here are some helpful links to explore:
Places of interest on Orcas Island:
Moran State Park Turtleback mountain Mount Constitution Olga Village Eastsound Village Doe Bay Historical Museum History of Robert Moran and Rosario Resort Places of interest on San Juan Island :
San Juan Island's West Side Mount FinlaysonRoche Harbor mausoleum Lime Kiln State ParkSan Juan County Park Roche Harbor Resort Downtown Friday Harbor Related posts:
Senior Citizen's Day trip to the San Juans recommendations Accommodations:
Orcas Island bed and breakfasts San Juan Island bed and breakfasts 
