My, unscientific, untested hypothesis is that the rule set for Alpha 2 with only the one modification of using the original setup charts provided with the rules in the box, may balance things out. That is, one would use the original setup for the global 1940 game, but use the rule adjustments given in Alpha 2. (National Objectives, Non-Aggression Treaty, etc.)
Why?
1. There is no naval base in Queensland, thus, certain territories (specifically Hawaii and some of the middle easy, as well as the Philippines) are no longer in range of ships in SZ 54.
2. Japan gets SIGNIFICANTLY more aircraft.
3. The Allies also get more aircraft, but to no extent as much as the Japanese do, nor are they concentrated in one nation as the Japanese ones are.
4. The extra 7 aircraft Japan gets, compounded by 3 rounds of non-interference by America (and probably England and Australia as well) could make a HUGE difference in the campaign for the Russian far east and China.
5. The location of the Japanese transport in SZ 33 may make the conquest of New South Wales, Queensland or Hawaii more secure earlier in the game.
6. If for no other reason than America has 23 IPC less fleet, and Japan has 0 IPC less/more fleet but Japan has 7 extra aircraft but America only has 4 extra aircraft.
Point being, Japan gets A LOT more units by comparison than America does.
While this is mitigated by what India and Australia get, and while they play a prominant role in the original theory of Japanese containment, I feel (based only on the layout of the board) that these bonsus will be significantly less beneficial to the Allies and thus, perhaps, balance a theater of operations that is woefully out of balance currently.