Intake to Head gasket Mis alignment

I'm doing My first gasket match etc. following @318willrun (great tutorial)
When I align my intake gasket to one of the heads the bolt holes are misaligned by aprox. 1/8". So Im afraid that the intake manifold will not align with the ports when assembled.
Anyone run into this problem?
The gasket Lines up perfectly with the other head.
Is the gasket port hole higher or lower than the head port hole. Or is it slid to the left or right? IF the gasket sits higher, just raise the roof of the port in the head to match.