Sorry for the length of this but I figued this may help others, and I wanted to include image examples to help
Disclaimer, I don't use the mods folder for any of this
Before starting, I recommend throwing the folders, images and zone, into a .zip folder or .rar before editing them as a backup. They can stay in the root T5 folder as they won't interact with the game at all. In case you want to remove the mod, it's easier to delete the folders and pull out the backups.
If you're having problems with things like textures not showing up properly, you could try how I have it set up, which is messier but works. Inside the main folder of the mod you open the iw_42.iwd in winrar, which I personally use for this, I have no idea if something like 7zip works. You can take the images folder and put it in the root storage/T5 folder.
Here's a visual example of a chunk of the files in the said folder
If the custom weapons aren't working at all, you also need to make sure that inside the zone folder that you don't have a folder called Common. Whatever is in that folder, put it into the root zone folder, and I have found everyhing to work.
Another visual example of what it should roughly look like
This is when it's incorrectly set up