I have experienced wind buffeting at times in my 2000 Spec Miata. You know the kind that happens when one of your kids in the back seat of the family car opens a rear window while all other windows are closed and your eardrums complain. It happens at higher speeds (above 90MPH) and only at certain places on a race track which tells me that the wind direction may have something to do with it. It doesn't have to be an overly windy day for this to happen. Might happen on one straightaway on a track and not the other.
The hard top is fastened properly as far as I can tell and not tweaked in any way. I've played with the height of the top at the rear base and it doesn't seem to matter. It's strange and I have never experienced this in any other Spec Miata I have driven. I gotta believe that this slows the car down aerodynamically when it happens. Any ideas?