Only slightly. If you're worried about this, put a couple of small dowels in the head. I.e. When the manifold has been machined, offer it up to the head. The mounting holes may need filling. Look through the port at the head and get the manifold to sit as near as possible to the original position. Drill a couple of small holes, approx. at each end, through the manifold into the head. Put a interference fit dowel in the head and open up the manifold hole slightly. Now the manifold will always return to this position when you bolt it to the head. You can now match the ports together.