I recently bought a 1990 4Runner and reinstalled the factory air intake and on the valve cover to the right of the oil cap there is this port where a place where a tube connects from the air intake and I was curious as to if you folk knew what it was and if you could tell me how it effects the fuel economy and performance of the car

 

It's part of the PCV system. And it's critical that it operates as designed. If not, you're engine will slowly disintegrate from the inside out.