All of robogen's basic pieces should be at the same scale in the original 3d model, use the same/similar scale once you figure it out.
All I can say for now is it's time to start guesstimating, measure from your hip bone, about 1-2 inches down from your hip bone, to a inch above your knee cap, measure the side of your thigh, once you get that, convert it to centimeters, and try to play with the scale until you can get the bottom right corner of pepakura to show a similar height or length.
The longest measurement on the bottom right of the screen will by the height of the thigh, if the model is flipped sideways, it may be length or width, but which ever is longest for the thigh will be it's actual height when completed.
It's like making a AR, you know the AR is supposed to be a long weapon, so you know the largest measurement will be the length of the actual weapon.
I've had problems like you on certain pieces, so I started guesstimating and finally got it right for my whole suit, good luck to you
