You could have a point show a ToolTip when the mouse hovers over it.
Transparency can be handled using the Opacity directive.
Addressing your problem would generally be best done by creating a custom graphics using Graphics3D rather than making use of prepackaged functions like ListPointPlot3D since you are combining a variety of graphics types: Points, Lines, etc...
Here is a random example of the sort of thing that can be done:
data = Flatten[
Table[Tooltip[Point[#], #] &@{r Cos[t], r Sin[t], Sinc[r]}, {r, 0,
10, 0.5}, {t, 0, 2 Pi, 0.1}], 1];
Graphics3D[{data, Opacity[.5],
HalfPlane[{{0, 0, 0}, {1, 0, 0}}, {0, 1, 1}]},
BoxRatios -> {1, 1, 0.4`}, ImageSize -> 500]