I apologize for my silence on this, got kind of busy irl. So Scipio was 100% correct. Turns out when the server installed it did so with no game.ini . I used the one that he attached here.
After installing this and moving certain settings from gameusersettings.ini to game.ini I got most of my issues fixed. The only problem that remains is I cannot actually level flyers. But land movement, player movement and all of my breeding settings got fixed with his game.ini file, so huge thanks @Scipio164