My right shoulder does the clicking/popping thing when I lift my arm over my head. I also have pain with it, which sent me to the doctor a couple of weeks ago, after putting up with the discomfort for months. She diagnosed tendonitis, due to constant carrying of my baby. (I had trouble using a sling for the first four months or so of my baby's life, so I carried her in my arms as much as I could.) The doctor recommended the following:
--taking an anti-inflammatory medication (e.g., ibuprofen)
--icing your shoulder a couple of times a day for 10-15 minutes at a time (a bag of frozen peas works well for this)
--a brief set of exercises, preferably with a light set of free weights (Doc said 5 lb weights would be too heavy); the exercises include bicep curls, raising your arms straight over your head, and a shoulder-shrugging kind of move that is hard to describe in words
--AND, most importantly, use a carrier (sling, front carrier, etc.) as much as possible around the house.
My doctor, wise woman that she is, did not tell me to stop carrying my baby. She knows that's not possible. But, she did advise being more mindful of how I do it. I'd gotten very careless about holding my baby with one arm and doing things around the house with the other arm. That'll mess you up right quick!
Feel free to PM me if you want more details. I don't know if I described this very well. Also, please know I'm not diagnosing you. Maybe it's not tendonitis, so my advice wouldn't work. But, this thread jumped out at me because I was certain I had a rotator cuff injury too, so I had to respond.