I just remodeled the arch in Maya instead of Rhino. I was having some issues with transferring the file to Pepakura because Rhino is a N.U.R.B.S. modeling program and Maya is more accommodating for polygonal modeling.
Here I just continually manipulated a polygonal form by extruding one face, then transforming the shape with move, scale and rotation.
The file transfered perfectly to Pepakura! As you can see there are no red lines, which I had many of previously with my file from Rhino.
I have much fewer pieces than before because of this cleaner model.