When I read
"James Macrory, Lord of Bute was the son of Angus, Lord of Bute and Arran.1
He died in 1210 at Scotland, killed by the men of Skye, along with his father and two brothers."
I interpret it as James died, along with his father and two brothers,
I'm not an English speaker, but if the same sentence had been in Swedish, then my way of seeing it would be right.
X is the son of Y. He died bla bla bla, refers back to X, because of a dot, instead of a comma. The rest of the text says that both the father and also two brothers died, the brothers must be his brothers, not the fathers, because that would be, his father and two uncles.