Suggest you look to the State of Mississippi for information about immigrants who passed through their ports from Ireland but bound elsewhere - like Puerto Rico. Mississippi had its own "Ellis Island" where immigrants had to be processed and similar facilities existed in the Carolinas on the eastern seaboard, so looking into the state archives for Mississippi may help you track your ancestor. Here is web address to the state archives in question:
http://www.mdah.state.ms.us/arrec/gen_research.php