I'm also looking for a James MacDonald, born in the 1800's, who supposedly was from the Isle of Skye but came to Canada. His children were mainly born in and around Inverness County, Cape Breton and moved to Codroy and Heatherton, in Western Newfoundland. I don't have any information on him or his wife although I have read in marriage records for his children that his wife was Mary perhaps even Mary Jane. He has lots of descendants in Newfoundland but despite my search I haven't found anything so far. Perhaps our James' are related.
You could try Donald MacDonald at firstname.lastname@example.org
He has a lot of information and may be able to help.
If you can't find anything on your James, you're likely related to me and I'm also related to MacIsaacs, which I can't find either. If you want you can email me with your info and I'll keep it as part of my search. I understand the frustration of not having anything conclusive, but you might try Mac first. He's a dear. You can tell him I've sent you.