It's messy, and you'll have a lot of clutter hanging out in Pepakura purgatory, but it gets the job done relatively painlessly. When you scale up or down now, everything (including the unprinted stuff) gets scaled, but only what you have on the printed area will print out to be pep'ed.
Repeat the process with all the other parts you want to individually scale in their own file. Then just select/grab all the parts that aren't a part of that piece you just named the file for (so for example, for the 'Torso' file, remove everything from the page but the torso) and stick them outside of the printable area. Name them 'Arms', 'Torso', 'Legs', or whatever floats your boat.
What I do is make several copies of the bigger, all inclusive, file.
