I have the same problem with the GTM Stage 1 SC kit. I think you are referring to the the 3 holes on each side of the undertray where it meets the fender lining. The arrows pointing
UP in the picture.
I tried to make some adjustments but the IC piping on the passenger side and the remote thermostatic adapter on the driver side prevent me from using the OEM pop clips.
I tried to use well nuts this weekend and the holes are just too far off for that either. For now, I am using zip ties. You can see in the photo (white arrows) where the IC piping contacts the undertray and where the thermostatic adapter also contacts the undertray.
I have not had any problems with the rectangle piece or the three pop clips under it that hold it to the car and I
might have seen 140 on speed. However, I think well nuts for those three would be ideal. See arrows pointing
DOWN in the picture.