Solved
After removing the rear tailgate glass it appeared that the runner on the drivers side was actually catching the rear door itself, so I removed the spare wheel and it looks like the previous owner had reversed into something pushing the door in just enough to stop the window from going all the way down. So a strap round the spare wheel bracket then attached to my wife's car and I managed to pull the tailgate out the centimetre or so it needed to get clearance, and after fitting the window back in, it recalibrated straight away didn't even need to disconnect the battery again, so one very happy chappy here now it's all fixed.
And a big thanks guys for your help I wouldn't have stripped it down had it not been for your ideas.