One method is to put a bunch of seed in the same spot in the pot, and let them grow. In nature sometimes a pine cone gets buried just right and a clump of seedlings sprout. Let them grow up several years, then thin to the number you want. You can vary the heights of JBP seedlings the same age by pulling needles early or middle summer. Pull more needles off the ones you want to finish shorter, leave all the needles on the dominant tree. Selective pruning will also be necessary. When repotting, treat the roots as a single root system if the trees are in the correct positions.
Bark for JBP simply takes time, 5 years for the initial hint of bark, 10 years to begin to look like real bark, and something over 25 years for mature bark. No way to rush it, time is all that is needed.