Shoulder clunking on pull ups.... tough one unless I know how the exercise is being done. A clunking is usually a muscle's tendon strumming against a boney projection much like a guitar pick on a guitar string. Needless to say it is not a good situation for the tendon.
My guess would be a supraspinatus tendon due to an improperly set GH joint. My area of interest is the position of the humeral head and if it is more anterior (by => 2 inches) at rest. If it is I would suspect an anterior humeral glide due to a very tight infraspinatus and a shortened bicep setting the head of the humerous outside the "normal" position, leaving the supraspinatus tendon vulnerable to strumming.
If it isn't then I would look to the boney structures of the shoulder with special interest given to the active movements and positioning of the scapula. Since I can write a small book on this, and is nothing but a review of your education, I will save my keyboard from my index finger assault.
Treatment would be based on the history of trauma of the shoulder, the speed to return to activity, and the discipline of the person to do their self care.