your proposed ANA/Air Canada routing will not work.
ANA does not accept pets in the cabin - you will have to check the crate. Animals are never interlined, and your one-hour connection in NRT is too short to retrieve the kennel and re-check it with Air Canada.
Even with a longer connection, you will need to check the animal for the trip to NRT, and retrieve it there before re-checking with AC. This means passing through immigration and customs - you need to adhere to all regulations regarding animal import to Japan including permits and all.
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Air Canada's 787s are a royal pain with pet carriers. You simply do not have enough space unless you have (purchase) a second seat to place the carrier. All extra legroom seating is either bulkheads, exit rows or premium cabins, all of which are off limits to passengers with cabin pets.
I would not fly AC at all.