Cando,
I get my own broadband connection at home on the 26 Aug., then it will be easier for me to do my research.
Murdoch father was definitely Donald Macdonald as I got that direct from a Gaelic speaker from North Uist who had a record of his patronym.
Highlanders in the 17, 18 and 19 century never had surnames (males or females). They all had patronyms, which were not labels but family history shorthand. They gave the fathers name and also his fathers name, so the son always had three 'Christian' names and no surname. The same was true for women and there mothers etc. The prefix Mac in Gaelic means 'son of' and you probably know that. What you may not know that the prefix Mic can be translated as grandson of.
So Murdoch's Patronym would be Murdoch Mac Donald Mic X, where X was the first name of his father's father. If he needed further identity he would also say "of Clan Donald" or "of North Uist" either of which identified him as a son of the 'Lord of the Isles'.
Also it was standard practice to always name the first male child after the fathers father, the first female child after the mothers mother, the second male child after the mothers father and the second female child after the fathers mother. This was only altered when an already born child died. The next born same gender child was named after that dead child.
You can see that Murdoch followed this religiously, in that the first male child of both wives was named Donald, so this must be his fathers name. The girls names also clearly indicate his mothers name etc. The second Donald use name was probably Ewan and when he died very young the next male child was named after him.
I will attach a copy of Samuel's cert to show you what I mean.
Ken