I've not had to install j-pegs from a box, but I've had the ones off my bike a couple of times so this is from my experience.
There are more holes on the mounting plates than needed. Not sure why, maybe they're for the manufacturing jig. Make sure you've identified the correct two bolt holes to use. Near the pivot bolt hole, there will be a hole for the spring and ball. This serves as a detent to hold the pegs in the stored or deployed position.
Install the proper shims and such through the peg according to the manual and thread the pivot bolt in with the peg in the stored or deployed position. This helps keep the ball and spring in place.
Snug down the pivot bolt, but don't torque to final spec yet. Now install the front stop bolt. The un-threaded part of this bolt rests against the curved part of the peg as a travel limit in the deployed position. When you put your feet out on the pegs, you are pushing against this bolt. Check the the peg swings open and close freely and you can feel the ball and spring providing detent function. Torque down both bolts to spec and check one more time for binding.
hope that kinda makes sense......
good luck