Seems like something in the script isn't fixing the order of the glsl variables automatically, though the error ("This shader (with the current [preset name]) doesn't follow the uf_* variable order from Cemu itself, so it might've been messed with.") still got displayed.
Before I fix this problem with the script tomorrow (should be fine to continue to convert packs, just don't ignore the error thinking that it would be automatically fixed for now), I though that I would send this hotfix.
Since it's not possible to update 300+ shaders manually and automation was possible, I thought that I'd take the honor and create a script that's able to automatically convert all of the shaders to be cross-compatible with Vulkan. And change the graphic pack versions to version 4 of course.
Also, the script has some nifty testing code which compiled every shader as OpenGL and Vulkan, but for that see the details that I've written below.
**Here's the script that I've made to do all of this. No manual edits were needed:**
https://gist.github.com/Crementif/8d98a855b95f219d95298fb3db99deae