Pepakura 3 has a 'Measure Distance' tool - right-click on the unfold section of the program, select that function. You'll be able to then select two points of the torso and obtain the measurement in millimetres between those points.
I would suggest obtaining the width of your torso, from either side of the lowest point of your ribcage; and the width of your collarbone, from one side of your neck to the other. Then finding the corresponding points on the model, and resize as necessary. Unfortunately, I can't be of much more help to you with scaling - this is something you're going to have to work out on your own. Nobody on the 405th, without being there in person with you, will be able to set up your files in a way that will make them fit you the first time you work on them. You're just going to have to work as best you can, and work until you find a scale that suits you; believe me, you're not the first person by a long shot to fret over the scale of their project and then have to rebuild until it fits them. I've been through literally a dozen Mk V Scout helmet revisions until I found a scale that suited me the best, so don't be disheartened.
I wish you luck in your build.