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The shop wants me to mill the intake in order to get proper intake bolt alignment and use the paper gaskets along with the valley pan per AERA's and Hughes Engine's recommendations.

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As said they came from Ma with just the tin & many were good for years and people have used em bare and with gaskets. The Felpro gaskets are ~.030" iirc and the superformance gaskets are .015". What works for me is to confirm the head intake surface and the manifold surfaces are flat & use the .015" gaskets with some Permatex 99MA spray gasket adhesive "high tack" the red spray on stuff. On initial mockup I brush some dykem horizontally along the top and bottom of the head and intake ports with a turn up on the ends (you'll grasp that when you get there) and scribe a line in the dye with a scribe and a metal ruler for a straight horizontle line then mockup the intake/valley pan/paper gaskets in place dry and compare the height of the scribed lines at the turned up ends & see how far down the "slope" the intake has to come down further into the "V" for the ports to be in good alignment then I give that number to the shop & let them do the math. If you're gonna mill you might as well take some extra time & get the port alignment dead on (the butt dyno will feel it). this means the head/intake gasket surfaces are flat/port alignment is good/paper gaskets help the tin seal that way everything in that system is spot on. I take a skim cut on the intake if needed and then cut the head intake surface to achieve alignment that way the intake ain't specific to that eng (helpfull if it is an alum one that might get changed/sold at a later date). If iron I might take it all off of the intake if the head intake surface is flat as likely that intake will be there forever. EDIT I prefer using paper with the tin and port (& especially bolt hole) alignment will dictate whether you can use paper or not without milling. OE deck height/ Head/intake prior milling/head gasket thickness can be anywhere (mockup/measure twice)