If the manifold is in the correct spot in the picture you posted, you are about 1/3 of a hole off. That's what it looks like in the picture. With no gasket in there, you need to remove whatever the thickness of the gasket is you are going to use, plus another .030-.040 to make up for not being line up now.
In other words, if you put the manifold on with no gaskets and the holes lined up perfect, you only remove the thickness of the gasket. The intake is too wide without the gasket, so you need to remove the thickness of the gasket plus another .030-.040 to get it the correct width.
And that means you are taking the gasket thickness plus the extra amount off each side of the intake manifold. This happens all the time. Not abnormal at all. Some guys want to take it off the intake face of the head but I almost never do that.
