Hawkeye is this a D&D [?] cobra like in your sig. or a more well known B&B cobra. I own a B&B and I also have the clearance issue. My way around it was to mill off the bottom of a K&N billet air cleaner. I also cut the bottom off an edelbrock air cleaner. They both worked out good. I have the luxury of a tall hood scoop which came as an option. I would not mill the intake as the divided plenum is small enough. This would also negatively effect the turn radius causing a problem with air and fuel mixture.
I have thought of buying another hood and putting a low Harwood scoop on it
but that's just me.
I have an air cleaner that I modified to breath better. Look in my profile under Lou's pictures.
Lou