As a priority:
- replace leaders on all your combat ships from destroyers and above. The IJN is compact enough that you can do this without much issue.
- replace leaders in your divisions. High land, Insp and Leadership values are what you're looking for.
- change HQ assignment of key bases (Iwo Jima, Paramushiro-Jima, Okinawa etc)
- Buy out restricted units for the Pacific theatre
I haven't gone down to ship-level yet, but that is something I'll have to look at. At the moment I've just been making sure I have great TF leaders and I'm not disbanding the TF and "losing" the leader I paid for. That might be inefficient, though.
The biggest flaw I've found in my war machine, once I started looking at leaders, was in the air wings. I was getting aggravated with a couple Zero squadrons taking more casualties than I thought was dignified for IJN's reputation, and when I looked at their leaders, there were a few that were utterly abysmal (one guy had 38 Air!).
I'm also currently finagling with some Construction Companies that were stationed in Manchukuo and can be better used expanding key ports to keep the resource and oil taps open.