So does anyone know how to use DOOM3 mods for the BFG edition? Ive found quite a few and im having trouble getting them to actually work.

You could try [url=https://www.pcgamingwiki.com/wiki/Doom_3:_BFG_Edition#DOOM:_BFA_Edition]https://www.pcgamingwiki.com/wiki/Doom_3:_BFG_Edition#DOOM:_BFA_Edition[/url] but not all mods will work.

The BFG Edition removed game DLL support and uses a different file archive format. It's one reason why people sometimes ask for the original D3 on GOG, which will probably never happen. :-(