As a well organized (errrrrrr) belligerent from the git go, the Japanese were stunningly inept.
this is a yes and no kind of thing, depending on what you look at, specifically. WE (the Allies) were also more than a bit ..inept.. on numerous occasions, and fields (tactics, doctrine, etc.)
One place where the US does shine, (a little) is that we tried hard to achieve basic levels of standardization, both within and across the services. Sometimes, we even managed to actually DO it...
Our small arms were much better standardized than the Japanese, or even the Germans, who had standards but also used about every thing they captured, if it still worked, and in some cases, (such as with the SVT 40) they captured enough to equip entire units for which they produced 7.62x54R ammo (and German language training manuals, etc..)
Every nation has produced competent commanders, and some outstanding ones. Also every nation has produced its share of commanders who managed to snatch defeat from the jaws of victory.
The Japanese used what, to us, seems a bewildering array of rifle/machinegun rounds, in 6.5 & 7.7mm calibers. From the outside it sure looks like it must have been a nightmare. Upon reflection I think that from the inside, it wasn't so much a nightmare, as a persistent migraine...
Supply screw ups happen to everyone who has supply. But they happen a bit less when there are only two choices to choose from, as opposed to 5 (or more).
Some years ago I watched a "Tales of the Gun" episode about Japanese small arms. They had examples of all the main types (including the rare SMG) and they were all fired using original ammo. What impressed me most was that out of all of them, the ONLY one that fired a full magazine /clip/feed strip, etc. was the Arisaka bolt action. Everyone one of the machine guns, SMG, and pistols all had at least one jam/misfeed/failure to fire, or other malfunction. Now it is possible that the museum guy doing the firing might have added to the situation, but I don't think it was a major factor.
On the other hand, it might explain the Japanese preference for cold steel, and the belief that the warrior spirit would overcome equipment deficiencies...