New K&N air filter Modquad

Hi fellow riders,

I had posted previously that I installed a new K&N Modquad air filter. At first it seemed it wasn't working right and I thought I may need to re jet. Today I took it out for a ride and it ran great 1-5 gear. So then I took the air box lid off and loved the sound it makes. So I left it off because it was even more powerful and loud. I went riding for 2 hours and the only concern i had was a noise the engine seemed to make while riding fast. It makes a noise like cracking inside the engine like as if the metal is too hot? Is this because I'm running with the air box lid off? It did do it a little too though with it on. Please let me know what this could be. And also should I still re jet? Thanks.