I have a 68 with a muncie M21. It has the hurst shifter as well. The gear shifter hits the console in 2 and 4th but if I shift gently it does not hit the console. So after I am in 2nd or 4th gear it is not touching. It is the slack in the shifter that when you wiggle it, hits the console. When you shift at a normal rate (not super gentle) you end up hitting the console from the slack.
If it is due to slack, is it still worth looking at the alignment of the 3 rods? they look all lined up in neutral but maybe I need to re-center neutral reference and shift everything forward slightly? Is it possible that the rods are correctly aligned since every gear works fine but I still need to readjust the neutral reference to have the shifter a little more forward so 2nd and 4th don't touch the center console? I can take pictures tonight if that will help.