Have you actually tried removing your airfilter, holding it up against your AFM to see where the holes line up in your engine bay? My guess is those holes go to the original airbox support bracket holes and once you have the filter out of the way it will be apparent.
The cut out hole is for the original airbox ducting to go through and the cut out at the bottom is for the black boost pipe that goes up to the plenum.
Oh and if you're keeping it paint it shiny silver it will reflect the heat far better.
A forum community dedicated to Nissan Skyline owners and enthusiasts. Come join the discussion about performance, turbos, racing, parts, classifieds, modifications, troubleshooting, maintenance, and more!