(1) Only half of the dot is showing above the surface plot. How can I have the entire dot appear? Should I simply add a small amount to the z-coordinate?
(2) How can I get rid of the line connecting the dot and the label?
(3) How can I get rid of the background of the label (make background transparent)?
Yes, the easiest way is to add an offset. Rather than using ListPointPlot3D you could use Graphics3D so you have more control over the point and label.
Hi Rohit,
Thanks for your reply. When I Graphics3D I cannot combine fig1 and fig2 because fig1 has a reverse axis. I use ScalingFunctions -> {None, "Reverse"} in fig1. So, the following code places X outside the surface plot.