It's only World.img that contains textures (.nft) and models (.nif) of peds and other stuff.
The mod should come with those to change peds.
Just look for the ones you don't want to change (the peds have their name in the file, so they should be easy to spot), and don't replace them.
IMGTool is fine, but I'd recommend
IMGFactory, as it's much more modern-like, and allows you to easily drag and drop files.
However, due to it not having support, it will crash when opening it. You can fix it by disabling its access to the firewall.