Yup all I had to do was remove define bones and everything worked like a charm, thanks a lot!

Yes that is perfect! (and yes this is for Garry's Mod) Yeah sorry I guess this is just me being completely new to the Blender and Source modeling scene. Thank you so much for the help, hugely appreciated. Although I do have a few questions, I thought you needed $definebones for the bones to work. Also why do would you weight paint the physics mesh, I thought the physics model wouldn't update anyway

Whoops, apparently Steam removed my link in my first post, check there you'll see the model source file

Yeah I know, I just got confused between mesh object and vertex mesh. Anyway I'm still unsure what is going on with my model, any ideas?

I am not exporting in DMX files and every time I rename a bone it renames the vertex group anyway

I can't figure out why but after I exported this modified model the bones are rotated in weird directions, I've done this before with another model and it didn't cause me problems

Here's the model source file:
https:// mega.nz /file/ZHJlFazQ#Fx6uHHXBNXsPjhubpBTid7mdV0akcMAO9jNoqGBp0aM
(Just remove the spaces^)

Also the left one is what it is supposed to look like and the right one is what got exported:
https://imgur.com/a/eTxvXiu