Even without knowing anything about your John McPhee, I can assure you that he most definitely came from Scotland, and not France.
There were many McPhees in Quebec, especially in the 19th century. If you could give me more information, I may be able to connect you with one of the Quebec McPhees. Interestingly enough there was even a story in my own family to the effect that a John McPhee left Grenville, Quebec, and was never heard from again. Maybe we can make a connection.