That is a lousy fitting gasket. You need one that fits flat and aligns better.
I do not think that the machining marks in the intake are an issue at all.
Not only should the gasket align much better but it needs to be soft so that is compresses as you tighten the intake down.
The gasket IS the issue. I haven't looked for a gasket recently so I am not aware of what is available but I am thinking that something as simple as the plain-jane Victor without the Printo-o-seal is likely the best fit.
Looking at the first picture of just the intake, the impression left by the gaskets on the intake seem to indicate that the Print-o-seal ring is the issue. It is in fact overlaping or at least too close to the elongated bolt hole.
I did not take pictures of my Hall intake but it appears that there is a variation in either the casting or the machining of the gasket surfaces.
I'll look through my pictures and see if I can find anything that will confirm or deny that thought?
BUT my thought is that it is the gaskets themselves. The Print-o-seal blue ring thing on those gaskets is not working for your set up at all.