I'm not an Unity expert, so please forgive me if there's a better way to do this :)
As far as I know you won't be able to get the spawn positions of particles of an effect in C#.
What you can do though, is split your effect in two:
- the storm cloud
- the lightning
Have the lightning effect spawn just one lightning, and instantiate it multiple times from C#, at random positions, and spawn a light along with it each time ?
Side note: if you want your lightning particles to light-up the storm cloud particles, you could use spatial layers.
If you're interested in that but not sure on how to do it, please ask (ideally in a new topic), I'll try to put together an example.