That's disappointing, because the alignment of my headers with the cutouts is not even close currently. IMG_3208.jpg
and that is with the body seemingly pretty well aligned to the chassis. I was able to set the four nose bolts and begin working my way back to the bolts on the body around the driver and passengers footboxes.
You don't base the cutouts oh the header flange, you have to fit them to the pipes because as D Stand said by the time they exit the body they have already begun to make the curve rearward. Quite simply yours were greatly overcut. The cutout never extends into the flare. Something like this is quite typical: