Thanks for the nice backstory - it always brings a bit more depth to a tree.
The piece has an initial appeal that is quickly overshadowed by its problems. The tree does not fit the rock, neither in terms of the shape, size, color or texture of the rock, nor in terms of that particular species when it comes to things like the bark texture and color on the trunk and the roots, needle length (even when ultimately shortened to the max), and the general sense of "presence" a JBP can bring.
In the case of this particular composition, the specifics of this tree-rock matching also present problems. This rock is not particularly compelling or interesting. At least for the Chinese, the importance of the rock - the more stable and eternal element - far outweighs the importance of the tree, which often merely frames and compliments it. A JBP is such a commanding presence that it will overly dominate all but the most impressive of stones. This stone is plain and puny for such a tree.
The way the roots are placed around the rock here is also awkward looking, and they also do not look convincing in terms of telling a believable story about the origins of the tree.
Personally, I wouldn't see much sense in getting rid of the rock though - this tree would look even stranger without it.
What you might consider is the complete opposite of where you are heading with this tree, and unfortunately it looks like you may have already limited your options along these lines with your pruning. Hopefully not, but even if you have, you may still be able to correct that, although it will take a longer time span.
I would forget about all that foliage up high. Maybe leave it there for the time being, though, so the tree doesn't just die on you, but direct its energy downwards through balancing techniques. When/if you do remove it, do so in such a way that you will have jins there.
I would focus entirely on lower foliage (although what's left of it now doesn't offer much short-term hope), and have at least some of it sweep back along the rock over time to at least partially obscure those unsightly roots and that plain looking rock - so that what we do see pokes out mysteriously and allows the imagination to substitute something more attractive behind it. Selective pruning and early wiring of contortions into the young growth will also add eventual interest.
Once the vigor of the lower growth is established, start removing all that dominant stuff at the top, and then jin some deadwood elements up there coming up along and perhaps slightly over the top of the rock. That would be my general idea.
Hope that helps.