1. although I do admit that my left scapula is a problem in that the surrounding muscles get tight from time to time or are generally tighter than they should be (and I'm working on strengthening these for better stability), I don't think what you describe is the culprit in MY case.
2. My musculature "clunks" from time to time in and around the scapula but usually not associated with pain...what I describe as a "clunk" is more a band of muscle fibers that are tight or knotted that need release. The clunk, in MY case, merely can be moved back and forth or it may on its own move back and forth but there is no increase in the pain or a creation of pain. I know this tightness is not good but it has a low priority because it doesn't cause or create pain. Massage therapists and Chiros have said it is quite common.
3. What I call "clicking/snapping" are quite tiny...think about tapioca pudding bubble size and popping those. And it falls literally within a 1-2" area around my left clavicle as it meets the manubrium that or near the first rib as it meets the manubrium. It may be referred pain from underneath but the clicking/snapping seem to appear on the top of these structure (whereas the Brachial Plexus is underneath). It is clearly related or part of the TOS as I have costoclavicular syndrome as well ...what is weird, at least for me, is the TIMING of this flare up. I awake fine other than general tight muscles which aren't too painful...the day progresses with my shower, brushing teeth, having breakfast and within about 2-3 hours of waking this flare up starts along with the clicking/snapping..I can then stretch and work it and within about 30-45 minutes it disappears...only to return the next day at the same time. Weird. I'm still working on seeing if I can prevent it or shorten it's time as it is relatively a new thing I've noticed. I haven't seen anything on the internet about this particular phenomenon. If it continues, I will have my doctor actually FEEL it. I have communicated with him about it and I would guess he will be interested to palpate it to see if he can tell WHAT it is. So far it seems to have dumbfounded the few specialists I've talked with. It may be a sort of subluxation between the rib and the clavicle as it meets the sternum that just happens to surface at that hour and with all the stretching etc., seems to work its way back. I'm just not sure WHY at that particular hour and for only the 30-45 minutes this happens.