Connie, I had just come to GenForum to post a note on this very family line, and saw your post. Although I'm not related to this line, I am working on a project that involves this family.
The person I'm working on is a son of James and "Ellen" FLANNIGAN whom I have not seen mentioned as far back as the 1860 census in Greenland Twp, Ontonagon Co, MI. However, I have a newspaper clipping from a Chicago publication in 1907 reporting the reading of a will that indicates that Richard C. FLANNIGAN of Norway MI and his sister at the same residence, Agatha FLANNIGAN, as well as a brother, John in Leadville CO, were siblings of Father Patrick Michael FLANNIGAN, the pastor of the former St. Anne's Catholic church in Chicago.
The beginning of the series, and the first section of the newspaper clipping are on the post preceding the entry for the link above. I will continue posting what I'm finding on the family as I work my way through the research, putting on my blog as I go.
Do you have your family data posted online anywhere? Are you on Ancestry.com or Rootsweb? I have not been able to determine who the "Katie Cook" of Iron Mtn is that was mentioned in the will. She is a niece of the priest, but I don't know who her parents were.
I'd welcome any info you can provide to fill in the blanks. I don't know if you were aware of the family connection to Fr. Patrick Flannigan. I have not seen any online genealogy records connecting him to the family other than that news clipping from my husband's grandmother's papers. I am also trying to pursue James' information from Ireland--who were his siblings and parents? If you know any of this, I'd love to hear from you!