From what I recall, it was actually model work for most of the Japanese and American ships with USS Yorktown (CV-10) used for the scenes of Japanese aircraft taking off of "Kaga" while USS Ticonderoga (CV-14) was used as a standing for Enterprise (CV-6) in close ups, with USS Kearsarge (CV-33) used for Enterprise entering Pearl Harbor near the end of the film.
"Akagi" and "Nagato" were sets I think in Japan.
At least that is one version of the events.
USS Wasp (CV-18) was deployed in the Atlantic during the filming of this movie.
USS Lexington (CV-16) was already a training carrier by this point and stationed in Florida.
USS Hornet (CV-12) was in the area at that time. She was being used to recover Apollo space flights that landed in the ocean. Picking up both Apollo 11 and Apollo 12 in 1969.
Wasp, where? Hiryuu? That's Hornet subbing for Souryuu.
Something's wrong!Nagumo's fleet, setting out!Akagi, you idiot!
Why are you running away?
Retake!Why don't you take a look at Hiryu?You just need to relax a bit.I want to take a shot of 4 IJN carriers going forward in full speed! Are the preparations in place?Wait a minute... I haven't trained well in walking backward.