Need help, advice with my 318 build

Are the header tubes going to be inside the holes in the flange? If so, then the hole area will be smaller.

I was taught that it was most important to avoid large increases in the exhaust port size from the valve to the end of the port, more important than a perfect match to the manifold, and that a modest step up in size to the manifold was not a problem. But, I am an amateur with porting, so perhaps some one more experienced will give the best advice.