Disastrously, I spent a long while working out why the chest joint was slanted. I noticed that the chest joint changed orientation the moment I tried to move the neck joint - but the tutorial video showed the neck joint being moved quite easily so I couldn't work out how to place the neck joint in the correct location without affecting the chest joint's orientation. My solution: unparent the neck joint, move it, then re-parent it back to the chest. Did it work? yes...so I went ahead with adding the "skincage" (advanced skeleton's auto-weighting tool)
...and then I realised nothing has actually been fixed! I now noticed the orientation of the hip and the shoulders were completely off. I don't understand how the person who made the tutorial video was able to freely move the joints without any problem but I was following the tutorial very closely and ended up with a twisted skincage. It took me another 5 new attempts at adjusting the fitskeleton, each time trying to avoid doing something that might affect the joint orientation and then I finally managed to generate a flawless skincage.
The answer? I didn't use the move manipulator tool AT ALL despite the tutorial video showing it was used. I merely adjusted the x/y/z values through the channel box and that seemed to be the only way I was able to avoid any disorientated joints. So I continued to follow the tutorial videos and ended up with a rather adequate rig of Caruso.
Some weight painting will still be needed (particularly around the shoulder/underarm area) and something needed to be done about the coat but all-in-all it was a working rig and I was happy it finally worked.
Now I can finally attempt to use the motion capture data we had spent hours recording in previous weeks. It has taken a very long time to get to this stage and there is still a lot of work to be done but first, I have a lot of learning to do...