No it wouldn't cause an air leak, but filing the hole would be my last choice/ option as I think something else is the issue. The seal is created between the intake runner and the port in the head with clamping force on the gasket, the bolt only supplies the clamping force not a seal. If filing is necessary we are talking about a few mils e.g., 0.010" not an 1/8". If a few mils doesn't get it home something else is wrong.

This is a long shot but are the manifold and the head being kept at roughly the same temp? e.g., the manifold was in a warm house and the head was in a cold garage? The intake is aluminum and would expand faster and more in the heat than steel.

You are working properly by not forcing the bolt and trying to figure it out.

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