Hi BristolBarb,
Alcatraz is a popular trip and having been there I can see why - when you get on the rock, if there is a chance to do a guided walk with one of the rangers I would certainly recommend it!
If you choose to take the trip on Day 2, the San Francisco by night tour with dinner departs at approx 6pm. And, after some more digging - The TM can offer two times for the Sausalito and Muir Woods excursions as they are operated by sightseeing company and these will depart either first thing in the morning (approx 9am) or around lunchtime (approx 2pm) and will last in the region of 4 hours.
This information would apply to both the 16th and 30th September dates.
Kindest regards,
Julia