I have never seen a plate or fender melted like that before
And yes , if you open up the airbox , then you will lean it out more than it is , so fix the issue before going that route
If the jetting is stock then its going to be real lean , that is how they are from the factory to pass emissions , so either just replace the jets , and needle , or get the JD kit , depending on what your budget allows , , as it will give 2 different needles , one for cold weather and one for warmer/hot weather , and a few different main jet sizes , i think they only come with 1 size pilot jet , but usually the stock main jet is too small , so it will need to be replaced no matter what , and depending on elevation , the pilot could also be too small
I would also suspect the needle to be causing a lean issue as well , it will most likely be set around where the 3rd clip position from the top position would be , so it would mean the needle takes more throttle input to allow more fuel to richen the system , by means of the taper and needle length , so a adjustable needle will allow you to fine tune the fuel delivery as well
The Fuel Screw i would replace with a R&D Flex Jet , it will make minor tuning much easier , and you will be able to adjust the fuel mixture while sitting on the bike , so it makes it real nice for tuning on the trail if needed (elevation or Temperature changes require fuel screw adjustment) , so that is the direction i would go , then report back with your findings , just do small adjustments/changes so you know what does what for better or worse