By the Roman Catholic parish records for Kingstown, do you mean these?:
https://registers.nli.ie/parishes/0523I have looked and could not see a Mary Anne Conway baptised on 14th October 1852. Apologies if I am missing something, but I just want to make sure our information matches. An Elizabeth, daughter of James and Teresa Conway was baptised on 14th November 1852 in Kingstown.
There is also another Elizabeth baptised in Kingstown to James & Teresa Conway on 14th June 1846, so perhaps this daughter died?
Also another child of theirs baptised 17th June 1855 in the same place; name is basically illegible as it is smudged but it could possibly be Richard.
I am also realising that the NLI registers don't seem to fully match up with the ones held by Ancestry, which is rather odd...
May I also ask what census you are referring to with your comment about Catherine? If you could provide links for all your statements then that would make it a lot easier for us RootsChatters to assist you.
Regarding the death of James, you are right that James is not listed as deceased on the marriage certificate, but he is also not described as living (like some of the other fathers on the same page) so I don't know if we can know for sure he was alive.
Queenie