All the clothing for CJ is in player.img, yeah.
Use tshirtwhite.txd as an example. Make sure you back it up before modifying anything, so if you don't like it you can change it back.
I use TXDWorkshop for my texturing, but you can use whatever you have.
You don't necessarily have to extract the actual .txd file, but what you can do is extract the actual image(s) inside the .txd file, in this instance tshirtwhite.txd; click "Export" up above the image, then export it to your preferred format (although a bitmap image is probably the best option) and save it somewhere, eg. your desktop. Then you can edit it to your heart's content.
When you're done, all you have to do is open up the .txd file again, click "Import" above the image and select your edited file. Then your mod should be in the game.
I hope that helps!