Man, that is going to be arduous to separate them. You have 50+, experiment with them! I have grown pine from seed for 5 years, and I grow hundreds each year, probably a few thousand the last 2 years. I also throw out hundreds. Dont be afraid to cull. They are cheap, and not alot of effort and resources has been put into them so far. Look at your 50+, I bet if you separated them into As, Bs, and Cs that the Cs would be about 50% of your numbers. Pitch them. They arent worth the time and effort of developing for 5-10 years. Now with the As and Bs, you can raffia some and wire them into funky shapes to account for the lack of needles/branches down low, but I think you will be surprised with how JBP respond to proper care. For example, I attached two separate pines in different age classes to illustrate what happens when you give them 9+ hours of full sun, water like crazy, and fertilize like crazy(all in the proper soil mix). All of my trees are grown from seedling cuttings, so the buds popping at the soil line probably wont happen for you, but I do think you will get buds along the 2"-12" of bare trunk you have now. The trees in my pics are 3-4 years old.
Your nebari is most likely going to be terrible. Now is as good a chance as you will ever have to correct it. I would focus my energy on nebari improvement, trunk movement, and re-invigorating these trees this season.