Make a big version!! I personally cannot stand Pepakura. These are drawing programs, not engineering programs. I honestly think Rhino 5.0 is easier to use, and not only could you make the model, you could make the ship, if you had the knowledge. Rhino prints out full size templates with marks on the paper so you can align small sheets into large scale templates.
With Rhino, you need a front, side, top, and bottom, orthogonic picture to reproduce it. Anything else is just speculation. That's a fact. Many models done in Pepakura are just plain off., unless the builder really knows how to tweak it. My 2 cents worth.