I had an Indy intake that wouldn't fit under the hood a few years ago. I just measured the amount it was too tall and had that much milled off at a machine shop. Cost about $75 if I remember correctly. Since I didn't have the chance to run both, I don't know what,if any, the performance penalty might have been. Or maybe cut the top flange off the adapter and have it welded to the intake after having the intake cut down till it all fits under the hood.

And I have had good luck with the Holley intake, myself.