Slim, I am sure that up until recently Cowie would have been pronounced as Coo-a. It is only as Scottish names have become more anglified that Cow-e has been adopted. The problem with your plantation theory is (and I am not an expert on this) most of the Ulster - Scots where lowland Scots. The Cowie's in origin where from North East Scotland, Banffshire and Aberdeenshire. Interesting you mention the Hugoneots again the French connection. I am not sure what you mean when you say;

"There were seven Coueys total on that ship. Three of their number had names with a French equivalent, yet they spelled them in the English fashion. They settled in the colony that was the focus of the Huguenot church in North America, yet they joined the Presbyterian Church".

The Huguenots where Calvinists and would have been at home in the Presbyterian church. The Huguenots arrived in Ireland about 1700 so if they stayed a couple of gerneration and went to South Carolina in 1750 would this not fir in?