yea it sucks, i noticed mine the other week when working on the car. The only thing I can even think of is to wrap the 2 corners it's rubbing on with reflective insulated piping adhesive (from home depot). It doesn't look too great, but it saves the intake a little. My friend wrapped his whole cold air intake w/ that stuff in hopes of getting the temperature of the intake down a few degrees (from some article he read).
other than that, I don't think the injen intake wants to go any lower.
or you could put adhesive or padding on the underhood.
I still have to fix mine, but the intakes already scarred

.