Manifold fitment question

When you mill the head (head gasket side) you also should mill the intake side of the head about 95%. So, .040 off head gasket side, take .038 off intake side. IMHO .040 likely will cause the intake manifold to not fit right. You could have trouble getting all/some of the bolts in. Sometimes elongating the holes in the intake will help. As for leaks (air, water, oil) sometimes these can be "fixed" with thick gaskets or RTV, but it's much easier to do it right the 1st time!