First, of all, thank you again.
I apologize for not having the file with me - it is 9:00 in New York and I will not be with it again until tonight.
That said, I was looking at Patrick John's birth certificate last night (which I acquired in 2001 from the records office), and it most definitely has his name as Patrick John McCall, born Jun 20 at the address cited above, with parents Patrick McCall and Juda McCall (and that is also listed as her maiden name.
I am 99% certain that I also have the marriage certificate of Patrick and Catherine Knox from 1888, and that this is how I learned that Patrick's father was dead and that Catherine had a previous marriage and children - I will confirm that tonight. It has been a decade since I looked at it, and have only started relooking at it now due to the recent passing of both of Patrick's grandchildren. I am also pretty sure that it says Patrick John McCall.
With all that said, I can also confirm that you have the right census listings for 1891 and 1901 - so the John McCall theory is certainly a new wrinkle proven by the 1891 census. Thomas was born in July of 1889 in Blackburn, and Andrew and Mary Vignole were Catherine's children from her first marriage.