I have never installed fenderwell headers, but since I am experienced with major automobile surgery, I feel able to comment.
I totally agree with cut small. In fact I would say measure twice, Think twice, picture in your mind twice then cut small. You should be able to lay the headers on top of the fenders with the flanges directly above where they will attach to get an idea of about where the hole will need to be whan measuring back from the core support. Same with the approximate vertical hole measurement. I'd hold the headers in front of the car, eyeball the approximate angle where the flange would fit against the head and approximate haw far down from the flange to start cutting the small hole. Then slowly but surely whittle on the hole. That's how I would do it.
