New EQ Head port 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.
For sure the heads and intake should be test fit on the block.
However, I’m not optimistic the port alignment would be very good, since the EQ ports are raised about .200” compared to a factory magnum head.