Those are the exhausts, which you said were recessed in your post. The intakes are positioned straight down, toward the piston and they are the ones which need to be moved deeper into the head. Nothing that I'm aware of needs to be done to the exhausts. It would be a good idea to install shorter pushrods for the intakes only, or shim the rocker stands and add a lash cap to the exhausts to retain the proper geometry for the rockers.
Jerry
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I tell my wife I have some timers. Some times I remember and some times I don't.
