Build and Shoot

I really need your help....

The easiest way that I have found is to simply save the .zip file you used to initially install the game, that way you always have the original files there in a neat little package.
From there you can go a few different routes. 1) Unzip the original game file and perform a fresh install, which wipes all installed mods 2) Unzip the original game file and install to a different directory than the one you use, then copy and paste the "fresh" install files you want, into the game directory you have you mods installed on. 3) I got tired of doing 1 and 2, so the last time I installed a fresh copy, I simply made some folders on my desktop and copy and pasted the "fresh" files to there, so that I would always have a fresh set of default files for my weapon/player skins

anyways, hope that helped

You don't need to change .pak files.
You just ignore them, and create mods at /Resources/ folder.

For example, one of folders look like: /Resources/Models/Weapons/Rifle/
Example: /Resources/Sounds/Weapons/SMG/
Example: /Resources/Scripts/Weapons/Spade/

Just take a peek into .pak files and you will see how folders should look.