Not sure if anyone checks back after years have passed, but I felt I should provide an update to all of those who helped!
I came across a new piece of information about our missing Patrick McCall. There is a record from the Chelsea Pensioners hospital from 1859 which lists a Patrick McCall from Drumgoon, Cavan who is in the military. I have also returned to look at the Currie family of Glasgow, in which a grandson named Patrick John McCall who fits the timeline of the confirmed birth of this Patrick Jr. in 1857 and lives with his grandparents in both 1861 and 1871. Of further interest, the witnesses at Patrick Jr.'s baptism are a William Murphy and what looks like a Sarah Currie.
Putting this all together, the most likely answer to my McCall problem is that Patrick Sr. had a child with Judith Currie in 1857 and then went into the military, leaving his son with his grandparents to be raised. There are no death records for anyone in this Currie family, so presumably sometime after 1871 the grandparents returned to Ireland. And I have no idea what happened to Judith.
This fits all the facts except one - the listing of "Juda McCaul" as the mother's maiden name on the birth and baptism documents. Juda fits with Judith. I cannot explain the McCaul, but I am tempted to chalk that up to the unknown under the weight of the rest of the evidence,