From: Connecticut, USA
OK, lots of questions. This is what I get for not showing up for a week or so.
Regarding production - the best answer I can give for most of your questions is I simply don't know. WPO was intended as a more streamlined version of the original WitP. The original game had a very detailed, and what some felt was very cumbersome, resource and production model. This is why you see aircraft engines and other stuff which have nothing to do with the game represented. WPO automated a lot of this. This results in some confusion in the manual, as well as buttons that do nothing in the game. In some cases you may have some limited control over what you can do, I just never took the time to see what works and what doesn't. I did always feel it silly that in 1929 the Japanese are still producing obsolete aircraft like the 1917 Sopwith Camel as opposed to cranking out more of the latest models. Same holds true for certain artillery - they'll have massive stockpiles of one but never enough of another. A limited amount of production management would have been welcome.
You are also way ahead of anything I've ever done as far as calculating daily allotment of fuel, etc. All I can fall back upon is the experiences I've had that Japan does run low in the late game if they're suffering from lack of oil resources or merchant shipping losses. I can't rule out some tweaking to fuel production wasn't done when WPO spun off from WitP - I just don't know. One mystery I never solved was what happens when you capture a base which produces oil resources? The (reduced) resource level is added to your overall tally, along with other things like industry, manpower, etc. Does the base slowly generate resources to pick up later? If so I never noticed it. Does the base move resources to a centralized location where it is combined with other bases' resources for transport to Tokyo? Or does it just automatically provide more oil resources for the Tokyo refineries? Again, I never delved deep enough to fully answer that question.
I'm not sure about moving fuel between islands, but I do note that at least on the Home Islands Japan seems to achieve some sort of equilibrium. If my fleet empties Hiroshima of fuel, I'll notice a spike of fuel in Tokyo shortly after. Not long after that, the fuel level in Tokyo will lower and that in Hiroshima will rise - so I know fuel is moving around on the Home Islands. The temporary spike is probably because oil is refined into fuel in Tokyo, and they're probably dipping into their reserves.
For me, ASW protection depends on how big the TF that is being protected, as well as mission, risk factors, etc. How many BBs and other large ships do you want in the TF? I have actually created 25-BB TFs for special missions before. Any remaining slots in the 25-ship limit I usually fill with DDs. If I'm playing Japanese in the late game, usually I'll use the later model DDs with good AA protection. If I'm not satisfied with the ASW protection in the TF, I may set a separate ASW TF to follow my high-value TF (or sometimes the opposite, have the high value TF follow the ASW TF). Or I'll create an Escort TF to follow as above. From what I've seen, the ASW TFs tend to be a bit more aggressive in their sub hunting, though the Escort TFs tend to provide more protection to the high-value TFs. There are no fool-proof ways of doing it, though. There's always a risk that one sub will pull a Gunther Prien and get a lucky hit on your favorite BB!