Perhaps you already have all this, Hatchetman, as I've just noticed that someone with Smallwoods research, submitted a pedigree resource file to familysearch on 25/08/2016, with John McGinley, Margaret Taylor plus children Sarah (and spouse), Alfred, and Robert (and spouse) all included?
The same file also has a John McGinley, born c1840, as father to a John born c1865 (seemingly the one married(?) to Margaret Taylor), and then a John James born 1876 and an Ellen born 1880.
I am still leaning towards there having been one John McGinley, born c 1848/50, father of John James, having possibly had two marriages and two sets of children or, given that in 1911 Margaret stated she had 8 children born and 6 living, that she was either his only wife and mother of all his children or she possibly brought some children into her marriage(?) with John, who took on his surname and believed him to be their father, and that she was perhaps a bit older than the census ages for her suggest.