1. If you want to add a pair of CAs, make them Mogamis, not Tones.
2. I would have Junyo and Hiyo as transports at the start of the war, especially since you want to add other CVs.
3. With Chitose and Chiyoda launched in '36, Mizuho in '38, and Nisshin in '41? I would leave them all as CSs. In fact, I would not allow them to convert. It would make an interesting scenario. CVL conversions were made out of necessity, not out of previous strategic planning. The scout cruiser was a big part of Japanese air naval doctrine.
4. 4x Aganos and 4x Oyodos, are ok.
5. Shinano should definitely not be built.
6. 2x BCs, 3 additional CVs (2x imp. Shokaku & 1x Taiho) may be a bit to much for Japanese naval industry. Even in exchange for not converting Junyo, Hiyo, and the 4x CSs, plus not building Shinano. But it's your mod... and I would definitely give it a try
7. If Yamamoto had such control, he probably would not allow army subs to be built. I have not checked if they appear in AE, but it is a thought.
Regarding carrier planes, if the A6M3 and the B6N1 are accelerated, that would give the IJN a HUGE advantage. I believe both would have been possible.
My 2 cents




