The Confederates, are basically still second rate, Like I said you can't run an army on cotton and oil alone. Florida may have been hard, but the confederates most likley would only be keeping loose control on mexico and and carribean so they could fight the Union.
Japan was in civil war, but was also in a period of rapid expansion, though maybe your right, and it might be more about 1900 until it was sold.
And I never said America developed the A-Bomb, I was thinking it might have turned into a joint ally project if they could get enough enthusiasm...Though I think Stalin was really intrested in nuclear power or bombs until after he saw what it could do.
However if you really want to take other things into account, perhaps the extra time added in the war, would have allowed Spain to rebuild some forces and enter in on the axis side, and possibly even Argentina or Portugal if things looked really good for the Hitler at some points. This could definatly lead to an axis victory, because even if this countries were second rate, the allies would still be overwhelmed.