Hey everyone, just a follow-up to this thread and some photos of the end result. I made some brackets that hold two air filters, a 1.75" from K&N (I found them on sale at MSA) and the standard 3.25" filter kit from Redline. Without the bracket, there was just over .5 inches of clearance, but with the additional filter bump there is now over 2". I got it assembled yesterday, and the car definitely breathes better, especially at higher RPMs. The last dyno test showed the airbox I was using was reducing the overall horsepower by about 10 (even when it was sucking in hot air from a non-moving car), and while I didn't put it on a dyno yesterday, I think these filters have almost the same result as running wide open. Also, I noticed that it goes more lean now at the higher RPM, so I can probably increase the main jet a bit. Seems to support the idea that it wasn't getting enough air before.
Incidentally, there wouldn't have been room for larger K&N filters as the master cylinder was in the way. Photos attached.