Keith, the port wall thickness at the pushrods is 0.050". I wouldn't go too far there. However, if you do break through, the oblong hole is sized so that a 3/4" OD piece of brass tubing can be used to sleeve it. You have to cut a 2"-3" section of the tubing, squash it oblong in the vise, and then pound it in there. I was actually planning on making an arbor to make the installation process easier, but no one has asked for one. If you port there and break through, and you want to try sleeving with an arbor, let me know.
The other mounting hole is not drilled only because a) the PSE manifold didn't have it drilled, so I didn't either, and b) it is kind of near the counterbore for the middle FE intake bolt. Hindsight being 20/20, those reasons aren't the greatest ones, and at some point in the future I plan to modify the CNC program to drill and tap the sixth hole. There is no reason you can't do that yourself, though, there is really nothing in the way there.
Hope that helps - Jay