When I originally measured up my NA to see if it would fit, I had a Cold Air Intake on my NA. There wasn't any interference, of course.
When I looked at it this afternoon, now that I have the OEM resonator back on the car, the situation as explained by ophidia31 is obvious. Yes, it could be worked around, but then the resonator wouldn't be stock any more.
My NA is a 1st 1000, and I want to keep it stock, or be able to return it to stock, so I don't want to modify the resonator as ophidia31 says can be done.