You'll probably know this anyway, since it's posted as a wip but the graininess here is coming from a lack of atmosphere samples. The cloud quality looks not too bad, maybe a little higher(there's a little grainy speckling in close-up white areas) but I'm assuming you've used the default 16 atmosphere samples. Try 32 for a big improvement and 45-64 for the final render.
Another idea to continue with might be to put an invisible light source at the point in the sky where you want to add the lightning afterwards. Lightning would illuminate the surrounding sky whereas, this one seems a bit to be floating in space.
