New EQ Head port misalignment?

This is what I did, with the heads off the car, and no valves in the heads, I bolted the intake on with and without the gasket and could see the drastic misalignment.

So even if one modifies the bolt holes in the gasket (as EQ suggested), that wont help any intake misalignment.
But you used the bolt holes in the heads, right?
If both heads are placed on a block, then the intake is placed on the heads with no bolts, we can see where the intake will "sit" on the heads and if the ports line up with intake. Again, ignoring the bolt holes. if everything lines up pretty close, just drill new holes.