Japan would have ultimately come out on top for the following reasons:
Germany relied on land advance, that is why it did not manage to conquer Britain, which had a superior fleet, leading to Germany resorting to asymmetrical warfare utilizing U-Boats in the Atlantic.
The Japanese had a better navy, and a superior naval aviation, distingiushed by unbelievably long-range airplanes. Japan probably had a better navy than Britain during World War II, meaning they could easily establish naval dominance in the Atlantic and establish naval bases from which great bombing raids could be conducted on German strongholds.
Germany was perfectly capable of building very good capital ships. Germany's problem in terms of surface ships was the fact that Hitler had to start over from scratch after Germany had been disarmed after WWI. Japan was not under any such limitation, and would go around the Washington Naval Treaty by converting the battleships/battlecruisers lost in that treaty into Aircraft Carriers. Germany was playing catch up and actually began WW2 five years too early, and as a result, many of the ships expected to participate in the European War were not yet built...
Much of this came because the limitations that hit Germany ran across the board after WWI. They couldn't have U-boats, dreadnoughts, military aircraft of any type, and I think heavy land weapons (tanks and heavy artillery). As a result, the Kriegesmarine battled with the Heer and Luftwaffe for material for shipbuilding as Germany built up the German war machine.
Even with this, however, Germany had built capital ships that were plenty effective against the Royal Navy. The British would deploy a fleet of warships with help from the French to hunt down the Admiral Graf Spee. When found off the River Platte, the German Pocket Battleship severely damaged all three British Cruisers before fleeing into Uraguay. Even with that though, the British never sank the German ship. Believing the Britsh had recieved massive reinforcements, the Graf Spee was scuttled.
Most of the British home fleet was deployed to hunt the Bismarck and Prince Eugen. And the opening battle of this fight involved a lucky hit that sank the Hood in six minutes and put the Prince of Wales out of action.
Had Germany won in Europe and been given time to recover, Germany could have very well replaced its WW2 and completed the H plan, which would have put battleships into service that would outweigh the Yamato. The turning to asymetrical warfare was not because the Royal Navy was "better," it was because the Royal Navy was larger when the war began in Europe. If Hitler had the fleet he wanted, he might have been far more willing to risk a Jutland-like engagement intended to sweep Britain from the sea.
And even if not, the use of submarine tactics would have devastated the Japanese. Just because it's asymetrical does not mean it is ineffective. Ton for ton, the submarine is the deadliest ship of war, and Japan neglected anti-submarine tactics badly.
And in terms of aircraft, I would not rate their aircraft as superior. Their pilots may have done better with carrier take off and landings, but one must remember that the Zero's range was mostly due to the fact that it had no armor and no self-sealing fuel tanks. Most German aircraft had those things. And assuming an Axis victory, you'd be matching largely piston engined aircraft from Japan against Me 262s and other German jet fighters after being given time to work the kinks in the engines out.
Another thing that would greatly boost the Japanese war effort is its possession of China and India, the greatest industrial powerhouses in the world. Using this, Japan could extend its already massive navy to create a presence in the Indian Ocean, as well as build up its army and equip it with tank forces which could match the Germans.
I'm not sure, but I don't think India or China were all that industrially developed at that time. Much of that industrial development came later. The industrial match up would between the Japanese factories on Honshu against the Ruhr and other heavily industrialized areas of Germany.
And Japanese tanks could not even face the Sherman. It is doubtful that they'd have anything that could take on a German Tiger tank...
And even if they did, remember that if given the time to develop it, Germany would have ultimately come out with a massively enlarged V-2 to serve as the first ICBM, possibly even nuclear armed.