Here is a thread where we were trying to figure out a similar trip. Our trip was also in September and it was a fine time to go. Overall nice weather and less crowds.
https://www.hobie.com/forums/viewtopic. ... an&start=0We car topped the TI instead of trailering and that mostly worked out well for the trip we did. We were gone for three weeks and the trailer would have been more of a hassle than car topping mostly because of motel stays and to some extent ferry's (you can take a trailer on a ferry - just cost more).
The main part of our TI sailing portion of the trip was about 9 days on San Juan Island and we stayed in a motel. Car topping definitely best here, parking the trailer would have been a huge hassle. We would sail every other day, do a hike or tour every other day. Near Friday harbor there was a free launch ramp that would have been nice to have the trailer for but we also sailed at Roche Harbor where the car top worked better.
We also took the outboard (2.5 Suzuki). I was worried about currents but after the first day, became much less concerned partly because of having the outboard along. There are a few spots that are known for high currents and at those spots, you should worry but for example we sailed from near Friday Harbor on San Juan Island to Lopez Island and currents were just not an issue. If you check tides and get that figured out, definitely not any sort of issue.