Thank you for engaging with me on this.
Stephen was tricky as well, but I found his family back in Ireland and proceeded from there. Just flew out to visit them last week, in fact. I can't remember every detail, but I think I found a memorial mass or something for his son Denis in a church bulletin. Then found his son's obit or something, and then his grave. Asked the local church secretary if she knew any of his immediate family that might still be living, and Stephen's granddaughter and his grandson's widow happened to be living nearby. From there, the living family helped me fill in the gaps on Stephen's girls, whose families have spread out to the four corners of the world by now. Stephen himself died in England in 1959.
Stephen's brother John died in Ealing in 1953, and for a long time I thought his line was extinct, but his oldest daughter did have a daughter who now has a thriving family in the London area.
Ellen is my 3x great grandmother and relocated to St. Louis.
Patrick, the oldest, seems to disappear after his 1858 baptism. May have died young, but I'm keeping an open mind on him.
Denis relocated to New York City and married Marie or Mary per family tradition, which is supported by a photo taken by Nellie's granddaughter of her visiting with him in Central Park in 1920. Can't find any remotely matching record for him, though.
Thomas's trail, as discussed, goes cold after 1901. I tried searching for additional kids in the GRO, but no luck, nor any later record for any of them that I can find.
Daniel also lived in NYC and married a Margarete per family tradition. I have an 1897 picture of him randomly taken in New Orleans. I've confirmed there is no matching person on any census of New Orleans. I did find a possible match in Queens. Had a daughter Marian and a son Daniel Vincent. Died 1925. Can't confirm it's him, as I haven't sprung for his death certificate yet.
Mary is said to have never married and stayed in Ireland. Not sure why she can't be found in 1911. The idea of trying to find her death certificate is pretty daunting given her extremely common name.
Unfortunately none of Stephen's descendants living in Ireland know about Stephen's siblings, despite their great-niece still being alive and relatively sharp. I thought she might at least know Mary, but it turns out she spent a lot of her youth in England, so she wasn't nearby.