Here's mine after almost 10,000 miles
Something is surely not right if you're getting that much heat in that location.
I'd check the radiator coolant to see if it's proportioned correctly for your climate.
I'd check to see if the cooling fan is working.
Do you have a fuel programmer? You did not list one, but usually if there's a pipe and airbox mods people recommend a fuel programmer.
I doubt being slightly lean would cause that kind of heat.
Are you sure that "melting" is not something that happened thanks to the previous owner? Can you contact the previous owner and ask what might have happened?
I don't think the exhaust/header has much to do with it unless they did not use the coupling spacer provided and there's a shit-load of exhaust gas escaping out at that location. You'd be able to feel it and hear it I'd think if that was the issue.
I have a stock header and an FmF Q4 pipe. I did not use any sealant at the connection between pipe and header, just the coupling spacer FmF provided.
You can see the condition of my wires.
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2008 WR250X
Gearing: 13t - 48t
Power Commander 5 / PC-V
Airbox Door Removed - Flapper glued - AIS removed
FmF Q4
Bridgestone Battlax BT-003rs