Found this
DOUGHERTY, John Willia 15 Jan 1881 Dou 302 DOUGHERTY, John FARGHER, Margaret Agnes
So looks like the John A is a red herring.
I wonder if on 1881 Census the middle initial should read 'H' as they were then calling him Herbert and mis transcribed?
Think the John A may be a cousin as looks like Alma is not unknown as a middle name
in the Daughertys.
Anyway, hope you get contact from other family members from your posting to find out more.
best wishes
Sandra