Thank you Chris,
I have dealt with the dust motes. I am sorry I was not clearer about that in the original post. As I mentioned there were dust specks 'inside' the protective glass lens. Once the lens was cleaned inside and out they have been eliminated.
The diagonal line is almost certainly something to do with the camera. It rotates with the camera always in the same orientation and shows up regardless of which filter is used.
Furthermore after cleaning and replacing the protective lens surely the lens would have been rotated yet the diagonal line remains in the same orientation.
Yes these issues can be dealt with using flats however the camera is pretty new.
You are right about the processed image having a lot going on. I need to look at each channels stack but I have noticed in a few recent images. I 'thought' it was condensation but I was sure to let the camera cool for a good 20 minutes before that last set.
Just thought maybe someone might have seen it before.