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I scrolled through the pages of the pay book and the pay for Penetang is there for 1840 but no Donald Fraser. The baptism is interesting as he may not have baptized for a few years if his father had died before.
Without knowing what William's mother's name was birth or marriage records aren't really helpful.
It seems like there just isn't enough info about Donald to trace him or his son.
I think the military pay book is the best clue.
Would there be a record of the burials from that cemetery for the year 1863?

I'm trying to find more about Donald Fraser born about 1811 and who died in Penetanguishene Ontario about 1862 or 63. Passed down from previous generations was that he was born in Inverness-shire Scotland to John Fraser (1772-1840) and Marjory Rose (1779-1850) and that he came to Canada about 1831. His wife is unknown but he had a son William D. Fraser who lived in Cleveland Ohio. Some of his siblings also came to Canada, Catherine (Smith) 1808-1887, Simon 1822-1857 and Angus 1821-1870 (deputy Sheriff in Goderich Ontario).
There is a tombstone in St. James-On-The-Lines Church Cemetery in Penetanguishene which may or may not be his. The date of death on it is June 2, 1863 and he is from Inverness-shire.

Thanks for that suggestion. I didn't know of that book and looked it up. Unfortunately it is out of stock on Amazon so I may not be able to get a copy of it here in Canada.
Her husbands gravestone is pretty clear with her name on it but it doesn't look like there was ever dates added to her name.

And I can't find Catherine in any census of her children and their families where she may have been at the time of the census. This leads me to believe that she died before 1841.