1. Take the strut tower brace completely off. I know of ton of people who have taken them off for one reason or another and my 94 Cobra never had one on it.
2. I believe there were certain strut tower braces that were made to clear those intakes. I don't know them off the top of my head but i know there are ones out there that will clear it. If i get a chance later today i'll look around to see if i can find one.