Just need to recreate the folder structure of where the files are supposed to go. It really is simple to make any mod JSGME ready :)
Edit: with JSGME I'm currently using HD Hog and Shark (blue) pits, BS backup ADI fix, NVG mod, Improved Clouds and Sky, Darker cloud shadows, Towns and Villages mod (incorporates Low and Slow textures), PeterP's viewport export files, Green Shkval, SweetFX...