From what I have read on boards--
Make sure you kow which port you are docking at. I know Carnival and RCl are at different ports which would affect transportation. I believe Carvial ship excursionsafterwards for instance drop you off at airport (which may or may not be helpful.) We have been to San Juan and a cab could easily take you to the Fort, old San Juan shopping in general. The El Yunque rainforest is I'd say at least 45 minutes away from docks. It is beautiful, however we had the ability to rent a car and tour early in day when we had the whole trail to ourselves and less heat, not a large group from a tour bus. If you like a moderate amount of exercise (walking) and beautiful scenery then that tour is for you. Do NOT forget bottled water though! I felt like I had gotten my aerobic exercise on that walking trail to look out area.
Bacardi Rum tour is very close to port--just walk a short distance and take ferry for less than a dollar. Then a small charge for a taxi to get to Bacardi plant. You used to be able to tour the actual factory now however from posts I read it sounds like more of a video of production.
Not sure if I covered everything you need to know, but a starting point.