Mike,
Living as I do in the San Juan Islands, I know the weather up here. The easy answer is, as always up here: "Who Knows".
However, having said that, I will say that the end of September can be the nicest weather we ever get (at least IMHO). The biggest dependable factor is that the days are considerably shorter. Almost certainly, as you say, it will be on the cool side. It could be rainy the whole week, altho big storms and wind are unlikely. OTOH, it could be beautiful fall weather with wonderful leaf color changes and warm yellow sunlight. Perhaps best of all there will be zero crowds. Almost very cove you see will be your own. Marinas are empty. The tourist atmosphere will be non-existent.
Here's one data point I use......in the 30+ years I've lived in Seattle and north, I use October 15th as the last day on a planned trip. Before boats, I used to backpack in the Cascades, off trail, a lot. So when using 10/15 as my date, I didn't take it lightly. Living on a C-Dory in poor weather is still much easier than stomping thru wet brush and sleeping in a damp sleeping bag! :wink: :lol:
P.S. If it makes any difference, my wife and I are planning to take a week long cruise up into Canada that last week of September ending with the Stuart Island gathering. So we'll be miserable right along with you. :twisted: