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To start, if you don't already have them, download Nem's Tools (GCFScape and VTFEdit). Searching "nems tools" should bring up what you want. In addition to these, you may also want an image manipulation software that's more refined than MSPaint. Gimp is a pretty good, free software you can download, and I could recommend it if you're not sure what to use, since it works well enough for me. Whatever the case, you're going to want to save in a few different file formats, so if your software needs an extension for .vtf and .tga formats, then be sure to get those as well.
With prep out of the way, first, use GCFScape to extract the files. When clicking on "extract" or the icon with the green arrow curving upward, you should navigate to C:\Program Files\Steam\steamapps\common\Team Fortress 2\tf (or where ever the games files are saved on your machine). Find the file that's called "tf2_textures_dir.vpk" and open it in GCFScape. It will then show you the compressed files and their directories. Things can get a bit confusing here, since there are many other texture files stored. The main ones you'll be looking for are in root\materials\models\player\[folder name here], where you'll want to pick the appropriately named lightwarp files from "demo", "engineer", "pyro", "shared", and "soldier". Some classes share lightwarps, so that simplifies a few things. You may also want to check in "items", but you probably won't need to unless you use a few specific all-class cosmetics (not sure which) or mvm loot. When you've found the lightwarp textures, right click on the files, and then click "Extract". It doesn't really matter where you save them, but it would be a good idea to set up a few folders that are structured like they were in the .vpk you just extracted from; you'll need to copy the exact structure and naming, or the game won't recognize that your mod is there. Also make sure to save a copy of said file structure, since you'll be saving the originals in one, and putting your mod into the other (this way, if something goes horribly wrong, you can always go back to the originals without having to find them again). You can rename your copied "root" folder to something that will help you remember the mod, since that name doesn't affect the mod's functionality.
Once you've gotten all the files extracted, open them up in your image editor of choice to do your thing. It might be a good idea to just do one at a time so you don't get confused what you're saving to where. It might also be a good idea to use the existing texture as a very general guide for how you should make yours, so that the areas where the light would get brighter can do so in-game accordingly. But if you want a very different feel, then by all means, freestyle it! Speaking of which, if you want to use different colors than the ones in the original files, feel free to do so, but I'll also offer a word of advice. Make the colors noticeably less saturated and slightly darker than what you think will look nice; in-game it may end up being quite the eye-sore with everything appearing extremely bright and uncomfortably saturated (think Lime Scunts and Pink as Hell Medic GF's, but cranked up to 12). But again, if that's what you're going for (like for a Hotline Miami -esque lightwarp, go for it!
Once you think you're satisfied with how it might look, export the images as .tga files and turn off RLE compression. Yes, you opened up .vtf files and are now saving as .tga, and that's because .tga is less likely to degrade the quality of the image by compressing it a bit less when exporting. Once done with that, open up those .tga files in VTFEdit by going to File... Import, and then locating them in the window pop up. You'll then be prompted with another window that essentially asks how you want the image to be displayed and read by the program. Under General Options, you'll want your Normal Format to be DXT5, Alpha Format to be BGRA8888, and your Texture Type to be Animated Texture (yes, even though it's not an animation). Also, you'll want to check the box that says Generate Mipmaps, and then set the Mipmap Filter to Quadratic and the Sharpen Filter to Shapen Soft. At the advice of another kind soul on this website, I've been using these settings to keep textures looking fairly tidy. Once all that is set, proceed to open the image, then once it loads, you'll probably want to check the boxes to the right that say Clamp S and Clamp T. I don't remember what this does, but I think it's kind of important. Once that's done, click the indigo-colored floppy icon near the toolbars to save/export this, and set it to the same place your .tga file is in, so that the game will be able to read the right file. And once you've gotten through all the files you have, it's time to test your mod! Unfortunately, it's unlikely your work will ever be done on the first try, since you will most likely feel like you need to tweak what you've done a bit. The process of trial and error can be a tedious and/or frustrating one, but once you've worked it out, you're set with a shiny, new mod that's exactly to your liking!
I understand that this may seem like a daunting task, but as long as you're patient and take your time, I can almost guarantee the end result will feel worth it!
If you have any problems feel free to reach out to me, and if I can't answer your questions, hopefully we can find you someone who can. Hope this was helpful and not too tough to understand!