Hi Lorraine
Can't see anything conclusive for you that would let you confirm at this stage James' death and family. As a merchant seaman, likely he may have died at sea. He seems to have been away from home for both 1851 and 1861.
Sometimes you can find some merchant seaman records on the National Archives site here:
www.nationalarchives.gov.uk/search/advanced_search.aspx?homepage=ad-search&javascriptenabled=True&j=tYou can deselect all and such search under 'Merchant shipping and seamen'.
I don't have any experience really of searching records for this occupation. Hopefully someone can give you further advice on this.
I can see a number of extensive family trees on this line on A/try. Looks like everyone is struggling with James' roots. Sometimes, when it is this hard, you have to look at alternative clues. Maybe not a 100% proof but looking for strong possibilities.
You are lucky that the family and the children are well researched. Their children are given as:
Samuel 1845
William 1847
John 1849
James 1852
Margaret 1855...fits well with the mention in Margaret's bc of 4 boys and 1 girl living at this time.
Grace McGuffie 1857
Archibald 1860
I found these entries for children and wondered whether connected to James' line - particularly with the mother's name (Grace and Grizel and interchangeable first name variants).
To Archibald Johnston and Grace/Grizel McGuffog (thinking here of James and Agnes' children born in 1857 and 1860):
1. Mary JOHNSTONE chr. 14 Jan. 1813 Sorbie, Wigtown
2. Grace JOHNSTON chr. 30 April 1817 Wigtown, Wigtown
3. JAMES JOHNSTON chr. 15 Sept 1819 Penninghame, Wigtown...wondered about this entry for your James?
4. Margaret JOHNSTON chr. 15 July 1821 Wigtown, Wigtown
Monica
PS: What is the source for James being originally from Minnigaff? The 1855 birth entry for Margaret shows Wigtownshire for James as his birth place (not more specific than than).