Hi Marybeth,
It is possible they used another name, but as she had a child in 1776 and one in 1798, it's unlikely there would be many missing baptisms before 1776 due to her age.
Mac is Gaelic for son of, nighean daughter of, mac-mic grandson of, and nighean-mhic granddaughter of. Mac can be abbreviated to mc, mk, or m'; nighean to nic, nik, or n'; grandchild to vic, vik, vc, vk, or v'. Neyn is a poor spelling of nighean. Gaelic never had a written form, except for ogham inscriptions, so it borrowed the Latin, and then the English alphabet. Which means spellings were based on fitting the sounds to the foreign letters, and consequently they varied. Today mac is the only term used, although nic is still used in parts of Ireland. A traditional Gaelic name used to be name mac[father] vic[grandfather] and then something like ņige (the younger), or bąn (the fair-haired).
I've looked at the Alexander/Jean family before, the names of their children appear to follow the tradition, which would make his parents John and Mary, but I can't find a family like this in Rannoch. The best fits are;
1749 Donald/Janet son Learan Fortingall
1749 Donald/Janet Alexander Killichonan Fortingall
1760 Donald/Janet Janet Ardlarich Fortingall
1761 Donald/ Janet Cameron Rachel Killichonan Fortingall
1748 John [Killichonan] + Christian [Liaran] Fortingall
1750 John/Christian Donald Liaran Fortingall
1751 John/Christian ... Alex in Rannoch Fortingall
1753 John /Christian Christian Aulich Fortingall
1754 John/Christian Margt Balnoe Fortingall
1754 John + Ann [in Learan] Fortingall
1755 John/Ann Duncan Newtown Fortingall
1759 John/Ann Alexander Liaran Fortingall
1761 John/Ann Ann? ...on Fortingall
1765 John/Ann Elizabeth Bailnoe of Learan Fortingall
1767 John/Ann Margt Bailno of Learan Fortingall
1769 John/Ann Christian Bailnoe Fortingall
And if he wasn't from Rannoch, but from the Balquhidder-Killin area, then the best fits are;
1738 John + Mary [Balquidder/Callendar]
1741 John + Mary [Balquhidder/Buchanan]
1742 John/Mary male child Kirkton Balquhidder
1743 ?John Murray/Mary Dugall Kirkton Of Balquhidder
1744 John Murray McGregor/Mary Alexander?? [cf 1745] Balquhidder
1746 John Murray McGregor/Mary Alexander head of Lochearn Balquhidder
1747 John Murray McGregor/.. McGregor child wright Lochearnhead Balquhidder
1749 John Murray McGregor/Mary Donald head of Lochearn Balquhidder
1753 John Murray McGregor/Mary Duncan Head of Lochearn Balquhidder
1756 John Murray McGregor/McGregor James + John head of Lochearn Balquhidder
1741 John + Mary [Balquhidder parish/Buchanan parish]
1742 John/...McGregor Janet Raynacraig Balquhidder
1743 John Buchanan/Mary Elizabeth Ruinacraig Balquhidder
1748 John Buchanan/Mary John Rhinacraig Balquhidder
1749 John Buchanan McGregor/...McGregor Katharine Rhinnicraig Balquhidder
1751 John McGregor Buchanan/Mary Alexander Rhinacraig Balquhidder
1754 John Buchanan McGregor/McGregor Mary Rhinicraig Balquhidder
Some of the families also have Duncans, so maybe one of them is your Duncan. But there's no evidence that Alexander is related to Duncan, and he may not be in the parish registers, after all his wife Jean isn't, but she is definitely the daughter of Ronald, as her funeral and her parents were recorded by a contemporary witness. This is the problem with guessing based on names, the historical record is incomplete.
The Rob Roy tradition in your husband's family may not mean a direct descent. It could mean the family was from the Glengyle clan, (most families in the area were), which is the family of Rob Roy. It could also mean they were part of Rob Roy's group, maybe originating from the north of Loch Lomond, Lock Katrine, Braes of Balquhidder, Strathfillan area. My family has the same tradition, but from what I can tell my ancestor was Rob Roy's cousin, not a son, and his family lived close to Rob Roy in the Braes.
John.