Alright so now I found it out on my own ;P It turns out I just had to unbind it from the original bones with ALT+P and then rejoin it with the correct bones after repositioning it, and everything fell into place!
But now I have a new problem, and I think it has to do with my QC file, because when I test the mod in game the arms of the character glitch out further from the screen in a bunch of stretched stuff I can't quite make of.
These are the screenshots I took of the glitched model
The first is the pickup
The second is firing
The third is reloading
The fourth is long distance from the front of the glitch "stuff"
The fifth is long distance from the side of glitch stuff
And finally the sixth is, although you can't quite make it out, the camera seems to be tilted to the right whenever I jump.
I really think it's the QC file, if that helps I could send it to any one of you for a look over of the entire general mod itself.