A few ideas/observations:

It looks like the replacement towers have a slightly uneven surface or flat surface. On the far right of the pic you can see a different reflectivity. Do you have the tools or a table to check the flatness of the tower? A pane of glass or a lapping surface, perhaps?

If it's flat, is also square with the holes?

Also, have you checked the bolts for trueness? And/or the holes in the head for thread size and cut?

Your last two pics are taken without the bolts in place, correct? If so, I don't think the problem is with the holes in the head, since they're not involved in that picture. That would leave the shaft, the rockers, or the cam as variables, wouldn't it?