I'm actually thinking the Graf Zeppelin remains in Kreigsmarine control with German crew. It would just be operating alongside the IJN and possibly start operating Japanese designs out of necessity since they would be easier to support locally.
That's fine, but it'd have to get out of Dodge before 1941. Look what happened to the Bismarck in May of 1941, and that was just going for a jaunt in the North Atlantic. Now instead you've got a more important ship trying to sail a whole lot further through even more foreign waters. Again, I'm not saying it couldn't be done, the German commerce raiders did it, but they had the advantage of disguise and many of them made their initial escapes in 1939 and '40, their departures growing more perilous as the war drew on.
I don't think that they'd actually have Japanese crews, mind you, at least for the delivery voyage. Officially, the Germans would likely officially discharge the crews from the Kreigsmarine, so that they could say it sailed with a civilian crew. I think the Germans could say they've sold it to the Japanese, paint a Japanese name on the ship, Japanese flags on the flight deck, and fly some Japanese flags from the mast, and they might get away with it if the Japanese used extreme diplomatic pressure. Once it arrived in the Pacific, I imagine that it'd operate with a composite crew, likely with a Japanese air group, complete with Japanese aircraft and flight crew. It wouldn't serve the Germans very much to actually sacrifice the aircraft and aircrew when they could use them back in Europe.
Interestingly, this "tale of two carriers" actually did happen, albeit on a miniature scale. The Germans operated a Japanese float plane with a German flight crew from the auxiliary cruiser
Orion to supplement their one remaining Arado Ar 196 until they received a replacement. Like the cruiser it operated from, it operated in disguise, in this case as a British floatplane.
Likewise, the Japanese operated an Arado Ar 196 in the Pacific, too. The Germans may also have even operated the Aichi E13A.
http://www.j-aircraft.com/research/stories/yasunaga1.htmlCheers,
Logan