Okay, so I might be completely crazy. I have two juniper shrubs in my front yard. They've been growing unrestricted for who knows how many years, and they had formed nice rounded mounds, about two feet tall and four feet diameter. I hate round shrubs.
So do I - if they are the same size and placed symmetrically. I have several round shrubs though, different species, each a different size and placed asymmatrically, and I think it looks great.
I cut out all of the low branches back to the trunk.
You did not add a photo, but it seems you got it wrong. You usually want to keep the lower branches.
They can serve different purposes: fatten up the base of the trunk, or form a new leader. But as said, you didn't add a photo.
So the problematic part of this project is that the foliage that's left is mostly at the ends of long, thin branches. My question is, can I get the foliage to grow on the branches closer to the trunk and is there any way to get new branches to grow lower on the trunk itself?
Nope. On Junipers (and other conifers) no new branches will grow on places where there's no foliage left. A branch without foliage is a dead branch. You have cut the lower branches, and, if no branches with foliage are left there, nothing will grow there. Only option could be to wire the branches and bend and shape them so the foliage gets closer to the trunk.
As you write you only have long, thin branches though, it sounds to me like the material is useless for bonsai.
I'll try to get a few pics up, but I wanted to see if anyone has any thoughts first. Thank you in advance for any advice!
Can't give you my thoughts, only my knowledge, without seeing the pictures.