Never, never, never use the SCALE field on pepakura to resize your papercraft armor, work with the dimensions is the right path to follow
There are two situations:
1st: The model was extracted from a game or you are sure that all parts were modeled by one person
in this situation you are sure that all parties have the same scale
then you have to take the following steps:
1. open each file on Pepakura
2. if it is not unfolded click unfold and then press ENTER (do not worry with the scale)
3. Now go in File>Export>press "3D model/UV info (*.OBJ)"
4. Choose a location with easy access and export each piece
5. open a 3d modeling program like 3ds max and import all parts for a single scene
*if the armor was modeled by a single person, all the pieces will appear to be on a similar scale (if you see a giant shoulder and a small thigh then you are in the second situation)
6. usually the pieces fit together automatically, if they are scattered around the scene use the tools "rotate" and "move" to put them in a human form
7. export the scene as a model in 3ds or OBJ format and open it in the Pepakura
8. you will see an armor like this:
9. Now you need to analyze the model, he has horns? the helmet is high? the model has high heels (like Raiden from MGRR)?
10. Now you need to convert your height to mm and add 50-70 mm in the case of armor with simple shoes and helmets, if the armor have helmets and shoes that influence on the size of the model you guys need to decide how much to add beyond the initial 50-70 mm
11. add the additional value to your height, click unfold and set that value in the "height" field
12. Copy the value displayed in the field scale and use it in the individual files for each piece of armor (2d menu> "recalculate parts layout" if the file are already unfolded)
this is the method I use, I never have to redo any piece
2nd: you are not sure if the models were made by the same person(That usually happens with Iron Man helmets and Halo armors)
in this case you need to use a photo from your character and make some proportions calcs to get the file size, for exemple:
print a Pic from Master chief where he is standing straight
take a ruler and measure the size of him in the picture (use milimeter or centimeter)
now measure his thigh
take your height + step 10 from 1st situation
now some mathematics
his height = a (you know)
his thigh = b (you know)
your Height = c (you know)
your thigh = x? (you don't know)
a --- b
c --- x
x= (b * c)/a
Now you have an approximate size of what would be the size of the piece on you
Put this value on Height filed and press "OK" (2d menu> "recalculate parts layout" if the file are already unfolded)