Problem Solved:
I had some conflicting directives going on.
In order to achieve what I needed I had to use the two calls:
yAxis2.orthogonalCoordinateDecimal = CPTDecimalFromFloat(0.0f);
y.orthogonalCoordinateDecimal = CPTDecimalFromFloat(maxEpoch); // maximum X value
x.orthogonalCoordinateDecimal = CPTDecimalFromFloat(0.0f);
Then in order to make sure everything could be seen correctly I had to play with the padding values:
float padding = 50.0f;
[graph.plotAreaFrame setPaddingLeft:padding];
[graph.plotAreaFrame setPaddingBottom:50.0f];
[graph.plotAreaFrame setPaddingRight:padding];
[graph.plotAreaFrame setPaddingTop:padding];
And I had to remove all the constraints that were messing with things:
// yAxis2.axisConstraints = [CPTConstraints constraintWithLowerOffset:40.0];
// y.axisConstraints = [CPTConstraints constraintWithUpperOffset:150.0];