I added a "clouds" variable to quickly add/remove clouds, without having to duplicate nodes. I also added a refresh button; if anyone is interested, I did this with a boolean export variable and setget; in the setter function I always reset it to false and refresh the particles & positioning.
I also added alpha fading by distance from the parent node, and when the alpha reaches zero, it resets. So, essentially, I now have a particle system of particle systems :) . To make the movement smoother, I added velocity/damping, this will make changes in wind direction look better. Lastly, I have a single wind direction variable (Vector3) that is normalized and used for updating cloud movement. Now the movement looks less random.

I will update the GitHub repository soon so you can see the code.