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.