Well, I'm actually more hands on with the 1/700 kits. For the most part, the changes needed are relatively small, depending on how far down the rabbit hole you care to go. The biggest difference is the aux. piping on BOTH sides of #1 funnel. Both 1/350 kits give you separate pieces, so you could fashion new piping from styrene rod or brass.I know there were some minor differences between Atago and Takao, but I am wondering: does the Atago kit have all the sprues in it needed to build it as a Takao? (I am looking at the 44 versions for both kits).
Technically speaking, their deck equipment layouts (particularly the mushroom vents) are not identical, and the Atago kit uses the Takao kit's main decking pieces. Some, not all, of the other minor changes illustrated below. From the Nihon no Gunkan vol. #6, the key from left to right is: Maya - Chokai - Atago - Takao