Finally, for re-emphasis here's the overview map of political control.
Japan Set Up Notes & Overall Strategy - Part II
The five "big picture" factors Japan has to think about, before thinking about individual fronts and sectors, are time, objectives, oil, production, and units.
Time
Time is almost, but not quite, on Japan's side. The Allies are the ones on the clock. Japan can win if they can't organize their conquest quickly enough.
In order to run the clock out on the Allies, Japan has to make them waste impulses and turns.
Japan can make the Allies waste impulses by sending out pickets of naval forces and "speed bumps" at the front. Japan can make them waste turns by ending them prematurely (e.g. by passing).
In addition, fortunately for Japan, the Western Allies are constrained by the ongoing war against Germany. Once the USSR is at war with Japan, it will not be so constrained as the kind of activities it needs to do to fight Japan (land moves and attacks) are the same ones it needs to do to fight Germany.
Objectives
Japan begins this scenario with 10 objectives. As I noted previously, it historically ended the war, at the time of its capitulation, with 9. The game rules expect Japan to have 5 at the end of the scenario for a draw.
Therefore, Japan's goal is to control 6 objectives at the end of the scenario. As such, Japan can afford to give up up to 4 objectives.
Truk and Rabaul, remote as they are, and given unit constraints (see below), are good choices to give up. The only difficulty is that they must be defended enough to cost the US precious time seizing them, but not well enough to make the Allies decide simply to bypass them. Over-committing to defend these two objectives may cost the Japanese if they do not have enough other units elsewhere.
All other objectives, in the meantime, must be defended as strongly as possible.
Japan should also look to the possibility of desperate grabs at Allied-controlled objectives: either a counter-attack against, say, an invasion of Truk, or attacking places such as Colombo, Aden, Dutch Harbour, Diego Suarez, or even Vladivostok. Of course, such ploys must be timed carefully so that, if successful, the Allies don't have time to recapture them or, if they do, they instead miss out on capturing one of the objectives in Japan's core area.
Oil
Of course, to be of any use, Japan's forces need oil. Unfortunately, while in a normal 1939 game Japan normally builds its synthetic oil plants (if that optional rule is in play), in this scenario Japan does not have any available. This means the 4 oil points in the Netherlands East Indies (NEI) are all Japan has to be getting on with (talk about your 'low-carb' diet). (Strictly speaking, Japan controls an oil in Burma, but I'm not expecting to be able to control it for long enough to benefit from it.)
Thus does the oil tail wag the strategy dog: to remain effective, Japan has to commit to keeping a convoy line open from its oil to each region it wishes to base oil-dependent units in, fighting off Allied raids against the convoy line, and defending the oil hexes themselves from invasion.
As such, Japan has to stockpile oil beyond its initial allotment (a mere 3 oil points). Tentatively, Japan plans to stock up on oil in Japan proper and in one alternate major port in the South China Sea. (Japan would like a third such stockpile, and will place initial oil accordingly, but I don't know if it will work out). Japan will try to keep discipline and save 1 oil per turn, 2 if at all possible.
Once Japan has a big enough stockpile (which may never be quite big enough) the NEI oil will be used for production.
The good news is that Japan only needs oil for 7 turns: it doesn't matter if it can reorganize units at the end of July/August 1945 or not.
Production
The other dog-wagging tail of Japanese strategy, the problem with Japanese production can be summed up as: Japan has 1 resource in Japan, and 14 factories to fill with resources, and if Japan can't produce units, it can't resist the Allied onslaught for long.
Japan has 19 factories: 14 in Japan, 2 in China, 2 in Manchuria, and 1 in Korea. Japan has 14 resources: 1 in Japan, 1 in Korea, 3 in Manchuria, 3 in China, 1 in Hainan, 1 in Formosa, 1 in the Philippines, 1 in Indochina, and 2 in Malaya. Of these, 8 must be shipped overseas by convoy point to get anywhere useful. If Japan can fill its factories, it produces 20 build points, a respectable total (if modest when compared to the amounts produced by the US).
Given Japan's reliance on convoy points to ship its resources, though, that is a very big if.
The bottom line is that Japan has to defend its resource shipping lines at sea, and it has to defends its resources on land.
Units
The Japanese Army is decently sized, but not numerous enough for its many commitments. Japan has to defend its production base in mainland Asia, its overseas objective hexes, and its oil. On top of that, Japan has to defend Japan proper from invasion, and would also like to scrape together a counter-strike force to repel Allied invasions of islands.
For its part, the Imperial Navy, while outclassed and outnumbered by the US Navy, is not insurmountably so - yet - and can still pack a punch, especially in combination with land-based air. Of course, the Navy guzzles oil, so if possible its use will be sparing - any turn where the Navy doesn't have to sortie will be a win, of sorts.
Japan's land based air forces are actually almost as numerous as their opposition, at least at the start of the scenario (depending on how much the Allies build to fight Japan, this may remain the case throughout, or it might change to a lesser or greater extent). These have to be placed carefully, as their primary objective will be to protect the convoy lines and the navy.
Where Japan really falls short is its sealift and shipping: it begins this scenario with but a single AMPH (amphibious craft) and a single TRS (sea transport) unit, and with but 14 convoy points. It gets more convoy points each turn as reinforcements, but any new sealift units constructed now arrive much too late (although, perhaps not...).
This Achilles heel really constrains Japan's ability to shuttle units from Japan to the periphery, or vice-versa, or to mount a counter-attack against an Allied invasion. It also means Japan has very little slack to replace losses, and can basically forget about keeping sea lines of communication open anywhere except the two core sea areas (the China Sea and South China Sea).