Thanks, Meryon!
There's a free edition of Gaea if you want to try it out and the Facebook group is very active, with lot's of people helping out, so give it a go. It is a lot of fun.
I'll do an in-depth video of the cloud trick, but the gist of it is to output separate passes for each light and the expose down the key light using a 3d noise as a mask. You can generate a 3d noise in nuke by using a Pworld or a deep pass. You get better edges with deep, but it's a bit more cumbersome if you are doing quick local renders I find.
This is the nuke gizmo I'm using atm is this one:
http://www.nukepedia.com/toolsets/3d/wptkmight end up doing a little gizmo that combines it all, I'll share if it happens