The scaling factor typically used is your height in inches divided by Master Chief's height in inches (88). Some people recommend adding 3-ish inches to your height for proper fitting and padding....
So, if you're around 5"6", you'd have a scaling factor of about .784, which you'd then multiply the dimensions by.
I think, at any rate. I haven't had a chance to play around with the Pepakura stuff I've d/led yet.