Your itinerary might be most easily accomplished by using a Vancouver Island launching point. I didn't read the whole thread and see if this was discussed, and I know that you would like yet another variable to add to your already complicated planning. If you launched on Vancouver Island, came to FH, returned to put yout boat back on the trailer and drove north, you could do the Broughtons, then trailer back to Nanaimo.
It sounds like a lot of trailering, and there is the expense of the ferries with a +40 foot setup, but it usually pencils out to being less gas and less time.
I think that most would agree that the trip from FH to PR or the Broughtons can be a bit of a slog. Even if the Straight is flat calm, and Seymour Narrows is flat and running your direction both times. You could use the mileage calculator that was just posted to estimate your fuel cost and time for a run on the water. Compare that to Google drive from Nanaimo to Port Hardy. My guess is trailering would be faster by a couple of days and cheaper by 100 gallons. That takes the bite out of the ferry fare.