Hello Louise: great to hear from you! You have actually supplied me with years of birth and death for John Allen that I didn't have. I can't add much, I'm afraid, to John's story, except that according to the marriage record, he was a Shoemaker by trade and I would have thought they would've lived in town, rather than at Three Trees, but as you say, all seven kids were born at Three Trees.
As you will have discovered, there are several Allen families in the district and there are also quite a few Weir families - many using the same given names generation by generation. As well as Rebecca, Margaret Allen, nee Weir (b. 31 Jan 1839 d. 19 May 1915 at Three Trees) also had a brother Robert Joseph b. 4 Jun 1853 - he never married and died on 8 Nov 1919 at Three Trees.
My great grandmother Rebecca b. 1 Jan 1848 married John Gallagher on 14 Feb 1878 at Greenbank Presbyterian Church, Muff Parish. She died in Glasgow on 14 Jan 1902 of pneumonia; her husband John was the informant, and indicated that both her parents were deceased at that time. John married again in 1912 and died in 1928.
Rebecca & John Gallagher (m. 14 Feb 1878 at Greenbank Presbyterian Church) had three children, all born in Ireland: two sons, Joseph (b. 10 Feb 1879, d. 18 Feb 1937), John, b.1884 d.1953 and Margaret Jane (my grandmother). They went to Scotland, and all three children married in Scotland: Joseph to Margaret McLellan and John to Elizabeth McMillan. Joseph and Margaret Gallagher had a son and two daughters; the two daughters never married and the son married but had no children: so that leaves my grandmother, Margaret Jane b.24 Dec 1888 d. 12 Jun 1974; she married John Anderson and had one daughter (my mother) and four sons, the last son dying either at birth or soon afterwards (they came to Australia in 1920). John and Elizabeth Gallagher married in 1910 and went to the USA. They had no living children (a daughter lived only two days). John died in 1953 and Elizabeth died in 1966. So that means that my line is the only one left from the marriage of John Gallagher and Rebecca Weir.
I hadn't considered the James Weir of Three Trees that you found - as you say, he could be a brother to Joseph, father of Margaret Weir: certainly the name he gave his son seems consistent.
I do hope this is helpful and will be happy to share anything I have with you. Regards Helen