I have found a way to fix the spatial reference so the scale is accurate when printed to my projection.
The problem now is that when I print the map prints larger then the defined box.
I think that it prints bigger to preserve the scale that has been set.
I tell it to print at 1=40 but when i compare the print to the slider it has actually printed the area of at 1=55 at 1=40 scale.
I am trying to wrap my head around this.
Do I just need to change the config file to match the new size of the print.