Had a great schedule when I booked the flight but they had to change flights. I fly out of EIS to San Jaun at 10:45, arriving at 11:30. The next flight is American at 1:10. To me this seems tight when you have to clear Customs and immigrations. What do you think?

Should be no problem if the flight is on time. Unless the flight runs more then 45 minutes late you will be fine.
G