DF, one thing to keep in mind is that any "Japan does better" thread has to be kept in the context of the fact (and yes I mean fact) that the Japanese still had no chance what so ever. Just look at the numbers:
http://www.combinedfleet.com/economic.htm
Also, prior to the Battle of the Coral Sea, the first five months of the Pacific War were pretty much a Japan Wank of the first order. That is why a lot of the Pacific War ATLs on this forum deal with the Allies doing better in the first five to six months of the Pacific War - because it's hard for the Allies to do much worse and there are a bunch of spots where things were closer run than they appear at first blush simply because of how much of a shoestring the Japanese were operating on.
The British were almost entirely focused on Europe, and the United States was spread across two theaters of operation, heavily focused on Europe. Lengthening and widening supply lines would have helped to mitigate some of the advantages held by the United States, but not all of them, and not in the long term.
Also, it's interesting to note that the one area where the IJN didn't significantly lag behind the USN was in submarines.
Like I said before, I like your idea at a macro level and I hope you pursue this but it's not going to win the war for the Japanese.
Imperial Japan was in a hard position because it could only "win" against the United States in the same way the CSA would have had to "win". In other words, it's a war in which one side has little to no hope of conquering the other power or even fighting a large portion of the war on its territory, but rather a defensive conflict in which it has to convince the other power that the costs of victory aren't worth it. The other side isn't going to run out of resources or manpower, the only asset it can really lose is the morale to continue the fight.
It's a good illustration of why the Japanese thought they needed to hit the British Empire and USN hard enough to make them quit the war. If the war lasted more than a year or two, they would inevitably lose. At the same time, they couldn't afford any major losses or defeats within that period.
The Type 93 could not be used on Japanese submarines. They loaded the type 95 with a range of 10,000 yards or less. The Long Lance was strictly a surface ships torpedo due to its size.
http://www.combinedfleet.com/torps.htm
The Type 95 is much better than the typical torpedoes of the period, but a submarine capable of carrying the Long Lance would have an even bigger advantage. I'm not sure how large such a submarine would have to be though, but it would probably be closer to modern submarine displacements.
Also, as others have pointed out, we should not overstate the impact Japanese submarines as well as surface ships and aircraft could have on Allied merchant shipping. For all of the hype about the success of German submarines in the war, the combined US-UK merchant fleets never dipped below 30 million tons and in July 1942 the tonnage of merchant shipping produced exceeded the tonnage sunk and that trend continued for the rest of the war.
Yes, US efforts to choke off Japan were ultimately effective but Japan's merchant fleet was only six million tons and they did not have the capacity to add significant tonnage once the war started.
Imagine if the Japanese and Germans had shared some of their submarine technologies and techniques with each other to maximize the threat? It wouldn't have been unprecedented, Germany shared some advanced technologies with the Japanese such as turbojets and rockets.
I think American torpedoes were so spectacularly terrible early in the war that any torpedo looked amazing.
I think most other navies simply designed them, tested them a few times to make sure they worked, and then put them into service. The Japanese conducted regular test firings in order to refine and perfect their torpedoes and other weapons, especially when budgets became constrained in the 1930s.
The ironic thing about building an advanced weapon is that cost or secrecy can make you hesitant to use it, so you never learn how to use it effectively or test to make sure it's still up to standards. It's not the last time that's happened either. More recently, it's been claimed that the reason why the AIM-54 Phoenix performed so poorly the few times it was fired was because it cost too much to do regular test firings and it was too advanced to be risked in most Cold War environments.