Japan Rework's Balance of Power shouldn't be Army VS Navy but...

Civilian government vs Military

In 1936, the game should lean heavily into civilian government but can be altered depending on the outcome of the February 26th incident. Slowly as the war in China begins and crawls, power should shift closer to the military like Finland's Mannerheim. If military grows too strong by 1941, then you unlock kamikaze attacks and, depending on how many islands in the Pacific it controls, increase homeland island defense to something insane like 50% defense (to represent Operation Downfall).

If you somehow manage to strengthen civilian government up until 1942 or 1943, it should allow Japan to call for peace against America and, depending on how many islands in the Pacific it owns, increase the likelihood of a white peace. It would be fun to try and balance the war with a civilian economy.

Civilian government should grant cheaper political advisors, more political power, civilian factory construction speed at the cost of soft attack and recruitable pop whereas military should grant naval speed, soft attack, recruitable pop and military factory construction speed at the cost of friendly casualties and slower MIO funds gain.

I could go on but I think you get the idea. I think the Army VS Navy could be done best as mutual exclusive focuses (so long as no repeats of Yamato or Zero in the old tree)

EDIT 1: Taking advice from u/ruhadir, once the civilian government or military reaches 100% they assume total control. For military, the balance of power shifts to a navy vs army; prioritizing navy helps supply consumption of the army and grants naval speed/attack etc at the cost of soft attack, production efficiency and cost.

Military control can lead down the fascist and monarchist tree, allowing the empowerment of the Emperor by a successful Kodoha coup or other focuses.

If the civilian government takes control, then its a balance between government against zaibatsu. Arguably full government could lend itself well to an anarcho-communist route with the main goal of destroying the zaibatsu (up for debate) where as government could appeal to leaning towards submitting to allies.