^ nailed it
For scaling, most people would recommend a program called armor Smith. You would have to pay some money (I beleive $20) and it allows you to take armor files and scale/position them on a 3d digital mannequin formed to your size and body shape. It is a great investment if you plan on doing more projects in the future. You can also opt to the method of measuring your arm or wherever your peice will go, from length and width, add an inch or so to the measurements, and scale the pepakura file. There is also a measure distance between two points tool in pepakura that can double check your peice.
Northern Dragon summer it up pretty good. Unfortunately you will have to go in and slide peices off of the paper in pepakura that you dont want to keep. There are some tutorials on the forums, and some great videos on YouTube to give you an idea. If I recall, heroes workshop had my favorite one. Keep in kind that where paper is 2d and may need to be the "walls" of some peices, the 3d foam will make up for it because it is tall if you get what I am saying...
And RandomRanger, I figured someone else could say this better than me. Where is the usual group anyway lately?
Follow this link and click the halo wars tab. It looks like these are foam ready conversions. Problem is is it is only the helmet and the chest... also just a tip, you dont need to cut out all the horizontal lines inside the specs of the chest. Those are there because pepakura thinks it should be paper and added them so the paper can fold into the shape. Foam can take that shape no matter what, so just trace the outline
