I hope that this may help you, I tried to look for the brothers of James -
Malcolm, John and Walter Logan to see if any of them could be found in America to narrow down the State where young John Logan was born.
1861
Malcolm - (born c. 1841 in Balfron) is working at Graystone Farm in Balfron
John - (born c. 1839 in Balfron) is living at home with James and Janet at Haldane Cottage in Bonhill
Walter - (born c. 1849 in Balfron) is living at home with James and Janet at Haldane Cottage in Bonhill
1871
Walter is living at home with James and Janet at Lamond's Land, Bonhill
John and Malcolm not found in 1871 in Scotland, no trace of Malcolm found after 1861 at all.
1881
Logan family in Bonhill as you know.
However, Walter may be the Walter Logan (born c. 1849 in Balfron), Stationary Engineer visiting the farm of William Wells in Inverkeithny, Banffshire. Also visiting is Elizabeth Logan (born c. 1852 in Forgue) and Margaret Resick (born c. 1811 in Forgue). I think that they are Walter's wife and mother-in-law respectively.
IGI has personal resource file showing that a Walter MacGregor (sic) Logan born 10th July 1849 in Stirlingshire, died 28th April 1921 in Berkeley, Alameda, California and was buried 30th April 1921 at Chapel Memories, Oakland, California.
Submission search shows that at a minimum he had a son born in Scotland in 1881 and a daughter born in 1893 in Alameda.
If he is your Walter, then he must have gone to California between 1881 and 1893 which doesn't fit with the return of James's family to Scotland sometime after 1874 but doesn't preclude his family as having been involved in the murder ... ok, see later, seems to have returned to Scotland and then back to California later.
Back to John Logan
On the 13th December 1861, Bonhill after Banns according to the Forms of the U.P. Church, John Logan aged 23, Dyeworks Labourer living at Mill of Haldane married Margaret Couborough, 21 year old Farm Servant living at Woodside. John was the son of James Logan, Watchman and Janet Logan m/s McGregor. Margaret was the daughter of Robert Couborough, Farmer, deceased and Helen Couborough, m/s Meikleham. (Interesting for me personally is that the witnesses were John Meikle and John Wotherspoon - both these people with Bonhill connection are in my tree.)
Next I checked for a death in Scotland using Margaret because of the name combination. I found only one dc for a Margaret Couborough Logan in all Scotland and sure enough she was married to a John Logan. Margaret Logan married to John Logan, Milk Salesman, died 11th February 1868 (aged 27 - so born c. 1841 and the right age) died of consumption after one year at 274, Garscube Road, Glasgow. Only problem is her parents - Robert Couborough, Farmer deceased and Grace Couborough m/s McIlquham. (Say it fast - could sound like Meikleham)
Although I wondered if the mother could be wrong or a step mother or .... I checked couborough.com only to find no record of any Helen Meikleham married to a Robert Couborough. Not conclusive but I couldn't find any Margaret Couborough with parents Robert and Helen in the census records preceding either. I am pretty sure that they are the same person, different spelling.
Ok, let's look at California. In 1880, living in Township 5, Amador (possibly transcription error), California there is a John Logan, aged 41 born c. 1839 in Scotland working as a Labourer in a Mill and with his wife Jane W. Logan aged 32, born c. 1848, also in Scotland. Living there also was his brother, Walter Logan, aged 30, born c. 1850 in Scotland, a single ENGINEER. I conclude that John married again after the death of Margaret but didn't find an mc in Scotland.
In 1900, Walter M(cGregor?) Logan is living with his wife Lizzie and family in Oakland Ward 1, Alameda, California. His year of immigration is shown as 1871 (Lizzie's is 1872, I don't know where they married, didn't find an mc in Scotland)
Also in the same household is is his sister-in-law, Jane L. Logan, born c. 1849 in Scotland and a WIDOW. Seems very likely that she is Jane, the wife of John Logan and he is deceased. Walter McGregor Logan of 960, 41st Street, Alameda was also registered to vote there in 1900. In 1920, Walter is living with his daughter Janet and son-in-law Emil C. Weston in Alameda. He is shown as married but Lizzie is not there with him, his year of immigration is given as 1869.
Just checked 1910, Walter appears to be a widower living with his brother - head of household is a B. Johnson (1930 census shows Brent Johnson, a Norwegian) and his wife is Jane L. (L for Logan?) Johnson, born Scotland c. 1850. Wonder if this is Jane Logan remarried?
Conclusion - if these Logan's are yours as they look to be, if the reason for James and family returning to Scotland was the murder of one of his brothers then the most likely brother to have been the victim was Malcolm. I base this on both John and Walter being alive in 1880 and the murder probably taking place between 1874/5 - birth of John Logan in USA and 1877 - birth of Ann Logan in Bonhill plus the disappearance of Malcolm after 1861.
Can you share with me who your Glens are?? If they came from Bonhill/Alexandria/Jamieston and/or surrounding, they are very likely to be mine also.
