Your plan of a week's charter with an instructional captain sounds perfect. The only fly in the ointment may be that chartering a Selene 47 will set the bar very high when it comes to a boat purchase.
There are so many options for a week in the San Juans that it really hard to give a set itinerary. I would imagine that the company that you are charting from would have some pretty tried and true itineraries for their boats.
One thing to look at is whether you want to spend more time anchoring vs marina visits. There are some very nice marine parks that are very good for anchoring. Friday Harbor or Roche Harbor are always a nice places to visit for marina stays.