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Too bad someone with a drill was allowed close to your bike. I have a starter cover, paint flaking off, with NO HOLES, that you are welcome to. Let me know if you want it, just pay for shipping - should be cheap, it's made of aluminum. I'm in SoCal.
Wasn't able to see exactly what you're talking about, but suspect they're what remains once the smog FRESH AIR garbage is removed. Best just to replace with an earlier non-smog cover.
If you click the cursor on the picture, it will give you a closer view, then you will be able to see the holes .