I was wondering if anyone knew what the little boxes are on top of the air intake tubes. When i get better air flow removing them and sealing the small whole or???? also if i cut my two brothers pipe down to a shorty, would i need to re-tune?

 

Those are called resonators. They minimize wind noise as the intake tubes suck in air. If you remove them, you'll end up with a whistling/wooshing sound & no increase in performance. With cutting down the pipe, I don't believe you'll need to re-tune.