What do you mean it doesn't specify? When you need to change the scale in pepakura you click on "2D Menu" at the top, then select "change scale" and then select "scale factor". A new window pops up and you can clearly see that there are 3 boxes for height, width and depth. I even covered this part already in my tutorial so I am a bit confused as to what you are talking about.
Do you mind showing me the file? If I take a look at what you got going on, I can help ya figure it out.