Quick update to the above:
I believe I may have found the issue with the CDJ on CH-1. When both L and R are connected, the audio in the headphones is perfect, it is only muffled on the speaker outputs. I think the reason for this, after some research, is that I am running into a single input on my audio interface, which I now realise runs in mono (panned either L or R depending on which of the two inputs I use). I will be switching to two mono cables for L and R today, rather than the single stereo cable I am using at the moment. I am hopeful that this will fix the output issues.
Still no luck with the dead R channel on CDJ CH-2 however. WIll be a real shame if this is simply broken.
Advice would still be appreciated, I'm quite new to all this.
Thanks, Matt.