You're making a texture pack for Dolphin 4.0.0? I wouldn't do that. Everyone uses Dolphin 5.0 (everyone should, since only 5.0 or newer is supported). Dolphin 4.0.0 and 4.0.2 uses an old naming system for textures. The only way we can help you with your issues is by updating Dolphin to 5.0 or newer. Otherwise there is nothing that can be done and you would have to deal with the imperfections of 4.0.0. Dolphin was never meant to be played with DirectX 9, it was just the only available option back in that time.
In other words, a texture pack you make for Dolphin 4.0 won't be usable for Dolphin 5.0. You should check this thread https://forums.dolphin-emu.org/Thread-dolphin-custom-textures-info for more information on Dolphin new Tex format for Custom Textures and the improvements that have been made for texture packs. This system was added since Dolphin 4.0-5234. The old Custom Textures system is flawed, and a common issue was that textures were not loading or only were loading when using the same texture cache accuracy speed setting they were dumped in.
Well... It is possible to convert the textures made for Dolphin 4.0 for the new Tex format, but it is a pain. So upgrade your PC with support for D3D11 (D3D12 is even better, DirectX 9 is a nightmare for Starfox Adventures). Get a better CPU, go get atleast 16 GB of RAM (8 GB works for smaller texture packs too) so you can prefetch texture packs (also new since Dolphin 5.0, which reduces stuttering) and get Dolphin 5.0 so you can avoid making your texture pack twice. I doubt texture packs made for Dolphin 4.0 are that useful nowadays.
In other words, a texture pack you make for Dolphin 4.0 won't be usable for Dolphin 5.0. You should check this thread https://forums.dolphin-emu.org/Thread-dolphin-custom-textures-info for more information on Dolphin new Tex format for Custom Textures and the improvements that have been made for texture packs. This system was added since Dolphin 4.0-5234. The old Custom Textures system is flawed, and a common issue was that textures were not loading or only were loading when using the same texture cache accuracy speed setting they were dumped in.
Well... It is possible to convert the textures made for Dolphin 4.0 for the new Tex format, but it is a pain. So upgrade your PC with support for D3D11 (D3D12 is even better, DirectX 9 is a nightmare for Starfox Adventures). Get a better CPU, go get atleast 16 GB of RAM (8 GB works for smaller texture packs too) so you can prefetch texture packs (also new since Dolphin 5.0, which reduces stuttering) and get Dolphin 5.0 so you can avoid making your texture pack twice. I doubt texture packs made for Dolphin 4.0 are that useful nowadays.