You might stick this in you back pocket for the moment.
According to http://www.ourroots.ca/e/viewpage.asp?id=603656
there was also a John McNaughton and a Donald McNaughton in Charlottenburg who might related. This comes from:
Title: The centennial of the settlement of Upper Canada by the United Empire Loyalists, 1784-1884 : the celebrations at Adolphustown, Toronto, and Niagara ; with an appendix containing a copy of the U.E. list, preserved in the Crown Lands Department at Toronto
Author: United Empire Loyalist Centennial Committee (Toronto, Ont.),
Publisher: Toronto, Ontario: Rose Publishing Company, 1885
On the Ancestral File (familysearch.org) there's an Alexander McNaughton b. 1817 (which is a bit late for yours) but the dates could be way out so it might be worth a look. At any rate, this is a Mcnaughton family in Williamstown and Charlottenburg so I might check it out.
It looks like the same Alexander is on the IG but with a b.d. of 1782 Williamstown. (that's quite a range for birth dates but the Ancestral File as well as the IGI are not always that reliable). Then again, there's a note about this Alexander marrying a Catherine or Anne Ferguson in 1803 so maybe I'm way off here too.
John Popham is also buried in Cassburn Cemetery along with Susan Maria (McNaughton). So it looks ike Susan was the dau of Alex & Helen. And it sounds like she was still around in 1896. So why don't any of these people show up on the 1871 or 1881 census?
.I'm afraid I'm striking out here - hopefully the burial records will help