Laguna 1.8 rn . r reg. HELP!!?

can u tell me wot would cause the engine to run rough and lose power in all gears below 2500rpm i have recently fitted a k&n cone filter could this be causin it. there is a pipe that went from the original air box to top of the inlet manifold can u tell me wot this is for and if this could b causin the problem as i have removed the original air box and its not attached to anything