Some thoughts for consideration.
Best approach from my personal perspective.
1. the first attempt did not turn out. I would replant the tree in a grow box, spreading out the nebari as best as possible at this time and work on regaining the health of the tree, it still has potential as a Bonsai.
2. Select a rock that has side perch and darker colouration and rougher contour so it becomes part of the display, not the focus or contrasting with the roots.
3. Do not plant on the top of the rock.
4. Start with younger material ( 1to 3 year old saplings ) and bind the roots tightly with lots of raffia. Before binding select a few stronger roots and position them carefully. Important to reduce the number and trimming away side roots not needed. Let grow in the ground/container for three years before disturbing. Lots of time to trim roots and expose slowly but the most important factor is that the roots form closely to the surface of the rock. Ideally in grooves or channels in the rock surface. Choose rocks that have these characteristics to begin with. Raffia is a better choice because with time it rots away, but it holds tightly for the period of time needed to form the roots to the rock, but not so long that is scars or prevents the roots from forming nicely. The extra time before disturbance also gives adequate time for the key roots to begin thickening to the point that they actually grip the rock.
5.Best material for Root over Rock has more radial roots to begin with and they have been reduced to a few stronger ones, odd number and unevenly spaced. I choose the sapling to fit the particular perch on the rock. Helps to have lots of saplings to choose from in the beginning. Best case scenario is a flat of saplings that were grown and prepared for this particular purpose. So the Root over Rock project actually begins with the way the seedlings are grown for the first couple of years and then matching the sapling to the available rock. Regardless of species the tap root has been cut and modified over the early years to make it suitable for Root over Rock.
Just additional observations for consideration.
Short version, I would not continue with that tree or that rock. And I prefer darker more neutral rock forms with contours and places to the side for planting rather than centred on top.
Thank you. I started this one 4 years ago with a very small seedling. I have learned a little bit since then. Apparently a lot of what I think I know doesn't make sense until I see how it fails. I have several of those 1st attempts that look better and some that look worse than this one.
One thing you are saying that does not get mentioned much is the importance of spending a couple of years prepping the plant material. I have discovered that a tree with a tap root is a mess to try to sort out later. One will have to remove the that big fat root at some point and then it will leave a gap that has to be dealt with. Starting from cuttings is easier than seedlings. I am looking forward to trying some crabapples from layers.
And the conundrum of selecting a rock . . .
Too small and it gets lost, too big and you can't carry it
Too plain and it is boring, too exciting and it either distracts from the tree or all the pretty gets covered up. Would a tree designed to show off a spectacular rock be an option?
Dark colored rocks show off light colored roots, but what color will my roots be? Pine roots look pretty dark to me but what will they look like after they are exposed and grow some bark? What about juniper roots? Can I assume they will all look about the same color as the tree bark? And would just a contrasting color look OK.
Anyway, I appreciate everyone's input. I cannot always see what is obvious to everyone else.