We took our 32' Islander up the west coast of Vancouver Island last year in June and had a great trip. We went mostly straight up to Tofeno, up into Clayoquot Sound, and back down through Barkley Sound. it was a great trip.
If the weathers good, the west coast isn't a bad place, I *think* you should be fine in September, but I'm sure more locals will chime in soon with more details on that.
Going out the straight can be a slog since you are going into the tides which makes them seem to change faster, so you get less of a push then when your coming back. Plus your into the winds as you mentioned, but that all just means coming back is easier then going out. Expect short steep waves at the end of the straight, especially as the tide turns to a flood.
Going into Tofeno was a bumpy and wet ride, confused seas coming from multiple directions as the swells changed. Not enough wind to keep the boat stable so we where rocking around good, and it was raining.
We weren't as prepared as we should have been in the foul weather gear department, and everything I had was wet by the time we came in, except one pair of jeans and a tee shirt. Lucky Tofeno has laundry at the marina. We where thinking of anchoring out, but easy access to dry cloths was well worth the marina fee and odd space we had to dock in, plus a nice guy with a heater on his boat invited us over for a hot cup of tea. What a wonderful cup of tea that was!
The rest of the trip was idealistic though, a little rain but mostly at night, and not the rough waves we had going up. Had a great sail back down from Barkley to the straight with a steady 15kts on the beam and smooth seas.
I know there's lots of issues with fog in July and August, hence why we went in June (And we don't have radar) but I think it's clearing up by September.
I also know the rule of thumb if your sailing south is leave the PNW by mid September, so I assume the weather would still be decent up there for a while, but I'm just guessing. Hopefully one of the locals will chime in and help you out soon.
Unless someone else knows otherwise, I would think that would be a great trip in September.