Ann: I wonder if I may have a link for William. I too am seeking my Nelligan ancestors. I have a John and Patrick Nelligan (born 1826 & 1829). They lived in Ontario, Canada. They married 2 Kieley sisters; Margaret and Catherine. I don't know if they married before or after arriving in Canada.
I have no trace of John and Patricks parents, nor do I know the names of any siblings. I wonder if William could be the father.
If William is the father then I have a large family history to offer you.
Thanks - Paul