Milling an intake manifold.
Just went through this exact scenario. Intake sat way too high because heads and block have been cut multiple times. My intake fit perfectly with no gaskets and my gaskets are .031” so I had .040” cut off the flanges and now it fits perfectly. I believe your thinking of taking .060” off is correct.
Maybe not on the cut, I had a stock 78 Power Wagon 318 never touched, bought it off the original owner, stock as a rock, even had 1978 dated plug wires.
The truck had 49,000 miles, engine such a grease ball, when I pressure washed it, the soft plug on the drivers head started seeping, the grease was holding the coolant in.
Anyways, went to bolt a virgin LD4B intake on, it would fit with the metal gaskets, but super tight with the felpro blue gaskets.
I did put it together with the metal gaskets, yeah I knew better, and yes after time it started leaking.
Tore the intake back off and managed after alot of cussing install it with the felpro gaskets.
I think alot of older aluminum intakes were designed off the cast intakes, when it comes to intake fitting.
The last intake I bought was a new Victor 340 and it fit perfect on slightly milled J heads with the Felpro 2113 gasket.