Lyric discussion by IrishToday 

A lot of the Irish when they immigrated to the U.S in the 1800s, established residency in places like New York and Boston (Prominently). They were able to crawl up the ranks of society but only after sacrificing parts of their culture. I think that's kind of what he's referring to. He "lost his leg" (lost something special to him i.e his culture), "climbing up the top sails" (climbing up the class ladder). But in the opposite sense, he's shipping off the Boston to "find his leg" too (i.e find financial security for himself and possibly his family in America).

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