We just booked the same cruise for late May next year. Here is what we plan.
San Juan is a late afternoon into evening port stop. We planned on touring Old San Juan and experiencing a little night life. (more research needed on the second part).
Just got back from St. Thomas and Tortola a few weeks ago (go to the Windjammer threads in the cruise section of this board and read about it). St Thomas of course has it's shopping, but, I would forgo that for a beach trip to Maegens Bay or Coki Beach (we will probably go to Coki) or a trip to any beach on St. John. Tortola is a great place, but hard to do a whole lot from 7 am to 2pm. If you stay on the Island, take a cab to Cane Garden Bay or one of the other beaches. We are going to take the ships' excursion to Virgin Gorda and go to the Baths.Beach, swimming, snorkeling and exploring through the rocks are fabulous here. A must do is a sandwich and the best Pina Colada on the face of the earth at Mad Dogs right where the cabs stop at the top of the path leading down to the Baths.