Just read that the IJN subs did not have a bathythermograph, this absolutely has to be disabled in the orderbar.cfg!!!
I made me a small addon for the IJN mod itself that makes the AI planes see subs at shallow depth and also adds the MK-24 Fido (copied from TMO) to their loadout (at the right historical date). Once I have finished my recent fleet-boat game (made me my own mega-mod with parts and fixes of all other mods + own stuff) I gonna return to the IJN again, so expect more reports and posts soon!
One more thing I read: The IJN subs did only start to have snorkels in 44, could they be be disabled before this date? Not sure if that's possible, just asking and giving ideas...
Oh and did you fix the (stock game) hydrophone/sonar bug mentioned in the OTC mod manual, the entries in the AIsensors.dat are switched so that the sensors behave wrong. A small thing but it could help to make the AI stronger.