Ooo, so there's lots of room for improvement here. It's going to be hard for anyone else to nail the look you're aiming for without a reference shot. But I think I can help with the smaller bits, and perhaps more importantly, I can give you some better render settings that will allow you to iterate and produce final frames faster so you can dial in the exact look you want much quicker. Assuming, that is, that you were using the "Test render FG Clouds" render node, which I don't know for sure as there are quite a few in here.
I'll start with the render settings first. So first off, I want to note that I'm going to suggest one or two quality settings that will change the look of your clouds a bit. I think this is overall for the better (and you can adjust other things to compensate).
In particular you are using a very, very low Ray-Marching Quality value in one of your cloud layers, 0.075 I believe. That's going to really cause the renderer to undersample that cloud layer, especially relative to the other one which actually has a rather high value of 1.3 or so, so you're going to get an odd mismatch in quality, and will have to crank up AA to get low noise in your cloud layer with very low ray-marching quality. Instead I'd suggest a value of 0.5 or so for both, and use AA and the global Voxel Scattering Quality (GI in Clouds tab of Renderer) to get quality up where you want it overall.
Now increasing the Ray-marching quality is what's going to change the look of your clouds. It will make one of your layers look more dense, at least it did in my tests. You can compensate for this by reducing the offset in the density function if you want, or adjusting cloud noise function Coverage Gamma (Tweaks tab), or other methods.
AA of 6 should be fine for a cloudscape like this. One of your renderers had AA12, hopefully you're not using that. You also don't need more than 0.25 or at most 0.5 for Micropoly Detail since you have no terrain and you're rendering the atmo with Defer, which doesn't use the Micropoly at all. That being said reducing it won't save you much, if any, render time. Likewise you can turn off GI Surface Details in the GI settings since it only applies to *surfaces*, and again while it won't save a lot of time, it does avoid a post processing pass and possibly reduce memory when disabled.
Finally, I'd suggest you consider increasing Voxel Scattering Quality to 100 *if* you have noise issues at AA6. But the default of 50 may be fine depending. I just don't think you need to go above AA to get noise-free clouds here.
Now on to tweaking the wispy bits. It's a bit unclear to me which parts you are concerned with, so I tried to address issues in two areas and you can choose which settings to adjust accordingly.
For the dark gray wisps that seem to appear randomly *below* the main cloud layer, that's coming from a secondary layer, and if you just enable Clamp Low in the Density tab on the "Density fractal Cumulus cloud01_1" noise function, you get rid of those. There are probably other ways, and this may make other changes you don't like, but from what I saw in the crop render area it pretty much just got rid of those wisps alone.
Now for the patchy bits of the *other* cloud layer, there are a couple of things you can do, depending on how significant the issue is for your need. First, reducing Roughness is always a good thing to try when you have too many small bits. It will of course have an overall effect, but it does tend to especially produce those little "flyaway" bits. Another thing to consider early on is the minimum scale of your noise functions. 5 meters may not seem too small, but if your cloud layers are quite far away it could add some very fine, wispy detail like you see here, so increasing that minimum value to for example 20 will get rid of some of the finer scale detail. Now admittedly this removes some detail from other areas of your clouds too, but if that's not desirable then perhaps focus on Roughness and noise type.
Consider also adjusting Noise Variation, though this will change the coverage of the cloud layer, which you can compensate for if desired by changing the Coverage Adjust. I recommend changing it in the noise function(s) rather than in the Cloud Layer.
I've attached a TGD showing the effects of some of these settings changes, along with a couple of images. The image file name that corresponds to the .tgd shows how that one in particular looks, of course.
- Oshyan