Belated reply, I somehow must have overlooked the email alert informing me of your September post, splinter.
Whilst Mary and the children sailed from Liverpool, it is not necessarily the case that they had moved there. Unfortunately, no passenger lists exist for that timescale for journeys between Ireland and England.
The closest census to 1854 would be the 1851. Only fragments survive for Ireland, but certainly there is no sign of John, Mary and the children in England at that time.
John's death, if it happened in Ireland, and as aghadowey has said, would not be on any civil index if it occured before Mary and the children emigrated, as none existed then. It may appear in a church record, but that depends on the individual church concerned, and again, what survives of their records.
It was interesting to read Mary's story, especially as it suggests her mother was a McComb to her maiden name. In 1849, a Thomas McComb married an Elis(z)a Smallwoods. To quote from another researcher:
"...Thomas was baptised at the Lower Cumber Church of Ireland on 14th August 1829. He was married there on November 28th 1849 to Elizabeth Smallwoods. Thomas and Jane had a daughter Jane on 22nd August 1850.
Thomas, Eliza known as Betsy and baby Jane emigrated first, when they sailed from Birkenhead. England, aboard the Mangerton on 27th January 1852. The ship arrived at Point Henry, Corio Bay, Geelong. Australia on June 5th 1852. Thomas and Eliza had another 12 children after arriving in Australia."
This quote and more of the McComb research can be read about at:
http://archiver.rootsweb.ancestry.com/th/read/MCCOMB/2003-06/1054901696and
http://wc.rootsweb.ancestry.com/cgi-bin/igm.cgi?op=GET&db=%2Dmy%2Dtree%2D&id=I1084