Hello and sorry about the late reply @Z0tikos and I completely missed this post in time, for faster replies you can just ping me on qhimm discord under FF7 > #axlrose-mods channel, I used KimeraCS by Lazaro, add the texture first, then inside the P editor select what texture to use.
Plus tons of the issues you are having I went through them with tons of help from Lazaro and others and is all in the chat history, with screenshots.
To fix the 3D meshes hmmm combination of KimeraCS and 3DS Max 2022, and to tell you the truth on the few scenes that I managed to line up correctly in game, I had to use my own version of the original textures that I upscaled myself, then on 3DS I aligned them correctly and re-rendered my new textures while modifying them in Photoshop and then exported again to .3DS then re-import back into KimeraCS, was a tedious job, only did for about 3 or 4 battle scenes this way, I still have to get to the rest and continue work on this mod, but I took a few months off to get some real life stuff done and take a break, I will continue with the rest once summer is over, but again you can find most of how I did it and figured out with help from others on that chat channel.