Nothing is wrong, 002 to 005 are parts of the first file and extract by themselves once you start the first, the file that comes out is missing the dot before the file type. It is supposed to be a 7z.
You should be able to change it the same way as you add it when creating a character.
It was probably an issue with mods that got updated for that build more than with RX4.1 itself. I don't have these problems, so it is specific to mods you use that I do not.
WinRAR or 7zip, extract the first file only and it will extract the rest automatically, then add a dot before the 7z on the end of the file that comes from that. Extract that and done.
Body tab in the creator, the mod is already applied.
Nobody really uses it anymore as we find it easier to use the repack, no having to install anything, mods already applied.
You could just not use any of the functions. Assuming you already have it installed, just set everything to the lowest setting or, if available, off. There is really only one function that acts by itself without the player needing to do anything, the automatic join thing that has girls join H scenes by themselves. All you have to do is move the bar in Kplug settings all the way to the left or right, whichever way has the number go down, I forgot which. The rest are only activated on player interaction. No, Kplug is not necessary, no mod is, but it enhances the game significantly. So much so that I couldn't even consider playing without it. Also, it shouldn't be messing with controls, it doesn't for me and I didn't mess with any key binds except for the mod that allows you to adjust a character's position in an H scene.
It extracted correctly, the file is missing the dot before the file type, should be a 7z.