How confident are you about son John's date? There is a Hugh Jones marrying a Jane Griffith at Nevyn, Carnarvonshire, 9 Feb 1849. At the time Hugh was a mariner, but his father Hugh was a farmer.
Just to mention in 1881 the above mentioned Hugh Jones is a farmer. IF John is the son of this couple he was likely illegitimate. Maybe that is why he went by John Griffith Jones..just a thought.
FH tree for family, but not checked details. The are a few others for same family.
https://www.ancestry.co.uk/family-tree/person/tree/168742127/person/352603420600/factsJust to add - I live in South Wales, but have travelled most all of Wales in my 60+, and as others have mentioned, I have never heard Caernavon shortened to Navan or similar. I would also go with Nefyn/Nevin.
Maybe DNA testing would help..just a few thoughts
Cas
