Yes, as I said it is a bit of a muddle of information, with huge gaping holes!!
When I was in my teens
well over 20 yrs ago, I had asked my great aunt (then in her 90s) for as much as she could remember about her family history.
For her father's family, there wasn't much, nor was it that coherent (she was lucid at the time, I just don't think she had enough information) Her memory of place for the Fergusons was not clear: She had started with bally or balla something (in Ireland, I later found out, that won't take you far!), she said they were from outside of Belfast. At one time she gave several possible endings for the Balla/y: Mina, Money, Mahar and Mackie. It was looking like Antrim... (I wrote this all down before I had access to anything other than a world atlas to look at) In notes I took another time, although around the same period, a name she gave was ballamahinch. Since Ballynahinch is the close to that, it seems all the more plausible now that it appears her grandmother was from Annahilt...
As for the "Sir" Black bit, I don't put too much stock in it but, while searching for clues, it won't help if I omit everything that seems unlikely either! Ideas like yours about freemasons or Knights of Malta might be helpful, indeed! Those are the kinds of things that can get a bit mixed up when stories are passed down.
My aunt's made a comment about Samuel's brother - the minister- "inheriting the family 'estate' "(while in his son's marriage certificate Samuel was noted as having been a "labourer"), seems grandiose as well. But I'm adding it because, in some twisted way, it might fit in! I don't have any name to go with the potential ministering sibbling and am short on dates unfortunately.
My aunt mentioned the name Annie Boyd, I'm not sure if it was as the mother of Samuel, but I'm truly not sure how she fits in. Having found a marriage for Agnes Boyd and Samuel Ferguson in Holywood (IGI), and a birth record (also IGI) for their child Annie that fits the age range of James' sister Annie, I got to thinking that perhaps Samuel married Annie Boyd instead of Agnes Black or perhaps after Agnes Black. Of course this may easily be a coincidence, as you say.
I've heard that many church records have been lost (something about them all being housed in one government building that was lost to a fire) so it might all be a wild goose chase anyway. Time will tell, I guess
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ard