I'm with Sean, I think that the people that lurk should join up, especially if they can do that caliber work off of anything freehand or pep. I'd like to see and hear how they do it that well cuz that higher level of precision is what I strive to do in all my work and I'd like to hear their tricks on how to make things look this good.
But I'm really gonna have to disagree with you Crucible on the fact that a Pep file cannot be modified. With a license for Pepakura Designer 3 you can export a PDO file as an STL, OBJ, or 3DS file. You can then very easily transform that mesh into whatever you want in a CAD program.
How I would modify the standard Wiki Recon file to look like the ones that Bungie received is by exporting it from Pepakura 3 as an STL file. Then import it into Rhino 4 where I can change the scale one dimensionally to make it a hair narrower down the middle just like the mystery helmet. From there I could then either pull on control points for the mesh or Cage Edit the front so that the visor was a bit wider and had more wraparound to it than the standard file. After a few touch ups here and there, I would then export the file from Rhino as an STL file, import it into Pepakura, unfold it, and then begin to assemble as normal. It's really not that hard to modify a pep file and I could probably modify the Recon file to look like this mystery build in less time than it took me to write this up here. Trust me, in the world of CAD modeling anything can be done and modified. How do you think people got the initial pep files to start with? By ripping the game models and editing them in CAD programs until they could be exported, unfolded and build to scale.
Just because you say it can't be done because you don't know how to do it doesn't mean that folks like us can't do it. Quite the opposite. We specialize in making your impossibility into pep files so that folks like you can use those files for free out of the goodness of our hearts.
Just my two cents.