Our 2 weeks with the Alaska Ferry system with 5 layovers are shown at the link in the signature.
We left Prince Rupert on a May 17. Made reservations the previous November. We played around with the schedule a lot and only needed a room on the Juneau-Sitka leg. There were no middle-of-the-night departures or arrivals but we also missed Wrangell and St. Petersburg.
We also worked in a trip to Prince of Wales Island from Ketchikan.
The best piece of advice that we ever had on this forum was to get more time in Sitka. We would have liked more time than our 4 nights there.