Coming to a dead end in Ireland is unsurprising. I see your note "It appears that Stephen and his Wife Agnes Howard were born in Ireland as potentially their two sons Robert and Stephen Howard." The best resource for church record transcripts name indexed online would be RootsIreland., but if Church of Ireland they may not survive, having been lost 1922.
As you just have born Ireland is hard to advise. However ScotlandsPeople's death certs should include their parents names to the best of the informant's knowledge so if Agnes was the informant on Stephen's death more likely to be correct than one of their children. As you have no dates or locations suggest you hunt for their deaths in Scotland and view images. Also look at the 1911 census for Stephen Howard as he is recorded on it. Though the 1881, 1891 & 1901 say born Bothwell, Lanarkshire, guessing you think possibly born Ireland as seems to be no birth reg or church baptism in Scotland.
GEMMELL, STEPHEN, aged 52, mother's maiden surname WILSON, registered 1874 Bothwell
https://www.rootschat.com/forum/index.php?topic=662800.0several possibilities for Agnes
GEMMELL, STEPHEN HOWARD, aged 54, mother's maiden surname HOWARD registered 1911
Coatbridge or Old Monkland
I see Stephen Howard Gemmell married 1881 Bothwell District and that his father was deceased but mother Agnes apparently alive
https://www.familysearch.org/en/tree/person/memories/LKY4-MNC and that the marriage was Church of Scotland ie Presbyterian.