I have sat the intake on the heads, make sure all the flat surfaces are clean and ding free, to check the alignment and then used a feeler gauge to measure all four corners with a feeler gauge at the top and bottom of the intake to head mating surfaces. don't be surprise to see some at zero and some as bad as .015+
Write the clearances down for each corner and then take that manifold to a good machine shop and have them surface it to cure the machining differences, if the bolt holes in the manifold are above the ones in the heads you may need to have additional material removed to get the port alignment better, if below then add gaskets (stack them if needed ) to raise the intake up to align the manifold