I understand you have to work the holes if the you are using an intake that doesn’t fit the one year only bolt pattern.
You need to find a way to look into the intake through the plenum and get a good look at how the floor of the intake matches up to the floor of the head.
From the picture you posted it appears that the intake is sitting too high. You can verify that by looking at it. If the port on the intake is high, you have to machine the intake manifold to correct the fit.