The plot thickens! I just found a death registration for a Thomas Armstrong, coal miner, married, who died 14 Jul 1860 in Dunfermline. His son, John was the not very helpful informant as there were no parents listed nor was the name of Thomas' wife. This Thomas' age is hard to read but it looks like 46 to me. If that's the case, this Thomas would be much closer in age to Mary.
I have found Thomas and John on the 1841 and 1851 census but no wife is with Thomas on either census.
1841 census - Parknook, Dunfermline, Fife
Thomas Armstrong, 20, coal miner, born in Fife
John Armstrong, 12 months, born in Fife
Janet Armstrong, 60, born in Fife
1851 census - 51 Store Row, Forth Iron Works, Carnock, Fife
Thomas Armstrong, head, 34, ironstone miner, born in Dunfermline
John Armstrong, son, 10, born in Dunfermline
There is a Sinclair family on the same page - Robert Sinclair (32, ironstone miner, Dunfermline), wife Jean (32, Dunfermline), daughter Isabella (10, Carnock) and son Thomas (7, Dunfermline).
I believe I may have found John Armstrong on the 1861 census living with a Sinclair family in Carnock:
No 25 Keepers Row, Carnock, Fife
John Sinclair, head, 52, coal miner, born in Dunfermline
Margaret Sinclair, wife, 52, born in Dunfermline
Grace Sinclair, daughter, 16, domestic servant, born in Dunfermline
George Sinclair, son, 6, born in Carnock
Agnes Sinclair, daughter, 4, born in Carnock
John Armstrong, boarder, 20, coal miner, born in Inverkeithing
Do you have a subscription to Ancestry? There is a private family tree that has John Armstrong in it. I can't tell for certain whether the person knows who John's mother was or what happened to him after 1861. When I did the search for John Armstrong, I included his father's name and put a first name of Mary for a mother and the tree was still in the results. If you don't have access to Ancestry, I could send a message to the person using the connection service for you. The worst thing that could happen, I suppose, is this Thomas Armstrong could be eliminated from consideration.
Jacquie