Wow, this is a tough one. I roof topped my tandem for a while, and it was quite easy, if time consuming...but I didn't have the added restriction of a high-top canopy on it. That being said, I launched and loaded mine by myself with my 1 ton truck (i.e., quite tall) with a hitch mounted cross bar.
I would say the biggest help you can give yourself would be to have some sort of guides on your canopy rack. Haul the front of the kayak up onto the canopy rack, supported from sliding sideways by the guides, and being supported at the back on the ground by a human of some sort, and just pull like hell (I assume you can stand on your tailgate to get the height). There are light duty electric winch systems as well that may help drag it onto your rack, especially if you make some sort of removable PVC cradle to guide it up.
I have a permanent mount, heavy duty Rhino rack system, and it easily held the weight of everything (along with the hitch mount deal). No clue if the Rhino boat loader type systems would actually work with the weight of our boats, but something to look into.
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