Xclavex, I really don't know why you're having those kind of issues. The only other thing I can think of is that you may have some kind of mod compatibility conflict happening. Verifying integrity wouldn't touch modded files in the root of your install, so look there and try to delete all files with the following extension:
*.lua
*.xtbl
*.asm_pc
*.str2_pc
Then reinstall your test mod and try again.
Wouldn't uninstalling the game and then manually deleting the saints row the third folder from the steam-apps directory have deleted those? I did that before I came to this site looking for help. Same problem. I don't understand it, I've done nothing else to the game, and if I don't run mods it works fine but every single time I try to add a mod, it crashes once I click on "load game" or "new game"