As the afternoon has gone on though he has been yelping and crying more and more, when getting on and off the sofa and when lying down, to the point where he wouldn't lie down at all. I took him for a short lead walk on his own again to see if he was lame and nothing. When we got back I tried to get him to lie down which he eventually did but he seemed not to want to stretch out his right shoulder so I'm guessing this is where the injury is. I have massaged it and put it through its full range of movement and nothing makes him yelp or flinch so I'm not certain it is this but I think it is. I wish sometimes they could just tell you whats wrong!
He is now asleep in the same spot I made him lie down in so I guess he is comfortable for now, lots of rest for Brian over the next few weeks and I'll keep a close eye on him to try and identify if it is that shoulder!