Hi btstuart09 and Forfarian,
First of all, thank you both so much for contacting me. I just looked here by chance, not expecting to find anything new (I've moved email providers, so didn't get a notification-oops!). This is definitely the right person, as the dates for everyone match with my records. I scoured the Scottish census information online and found a possible match for James on the 1841 Kirkmichael census (ED10, p3, line 1300), aged 14 and working as an agric. labourer in Kirkmichael on the farm of a James McPherson (60, farmer) and May (60). I wondered if James and May McPherson would be his grandparents: his mother's parents, John and Margaret (who was also known as Mary and Mary/ria). I then found an entry for a James Stuart, aged 21, on the 1851 census for a place called Rechlerich Farm, par of the Ballindalloch estate, which is a place name that was passed down in one branch of the family. I'm not too worried about the age discrepancy, as judging by many of the records I've seen, most people just took a guess at their approximate age most of the time. I've also learned not to pay too much heed to the spelling of names, as long as they are phonetically the same.
On the subject of the family split, I did wonder if it could have anything to do with religious differences? My Welsh aunties were quite shocked and upset to discover that their close ancestors had been Catholics, as they are pretty much all devout Methodists and always have been. I can only assume that James was likewise a practising Methodist, or my aunts would have known.
I have now amassed quite a bit of information myself on the broader family tree going back to John's parents, Donald and Margaret, and would be happy to share what I have if you are interested. I'm currently digging around trying to see if I can get any ideas for Donald's parents, but it's like trying to run up a hill covered in treacle!
Thanks again