Yes it seems only the first <150 Ki-43-II got the longer 43-I wings. So the il2 Ki-43-II represents the major production model ~2800.

But the il2 Ki-43-II Kai is a mess. The Ki-43-II Kai was an interim Nakajima design produced 4/1944-9/1944, only ~500, some even used water injected engine.
The Ki-43-III was built ~1100 starting 10/1944 at Tachikawa, all with Ha115-II water injected engine.

I have been using SFS file extracting tools and looking at SAS mods. They have proper Ha115-II engine with auto-water injection (system like Ki-84).

The easiest fix would be keeping the "coded" name KI_43_IIKAI for compatibility, but changing "game" name to Ki-43-III, and aliasing the Ha115-II engine for it, with ~100L MW tank behind pilot.

It is totally possible, and easy, to have an script which changes all mentions of the keyword KI_43_IIKAI to the keyword KI_43_IIIKAI in all mis files in all the folders of your Sturmovik installation. You could also change all mentions of KI 2 to KI 3 in the properties files.

The issue would be with all the mis files in the internet, like in M4T or patrulla-azul. I don't know HTML, so I don't know if it could be possible to change already uploaded files.

I have still been researching how to fix the il2 Ki-43-II Kai which as at 4.13.4 is still not right.

The Ki-43-II Kai all came with bomb racks which reduced speed to that of the earlier -II models, so Il-2 version is OK there....but then the bomb racks should be added to the 3D model, and the existing 3D exhausts pipes are still wrong as they are in the -III style.

It still seems much easier to alter some 20 lines of code to make it match its 3D model which is of a Ki-43-III, by aliasing the game name to Ki-43-III and adding the Ha-115-II water injected motor specifications, with 70 ltr H2O tank behind pilot.

I believe that the only way to fix this problem is to keep the old, incorrect, model and add the corrected model as a new plane. That was what was done with the badly-modeled early Hawk 81/P-40 series when we got a better replacement.