Since no one gave any feedback on this issue, I will. I'm just an athlete, not a doctor.

Painless shoulder clicking is often a sign of slight muscular imbalance or joint instability. I, and many people I have spoken with, have had success beating the clicks by strengthening the muscles that keep the shoulder pressed into the glenoid. Here is what I did:

1) Reduce weight and focus on strict, slow form. If your joints are complaining, it's often a sign that you're using too much weight.

2) perform prehab "injury prevention" exercises that strengthen the rotator cuff. Internal and external shoulder rotation with VERY LIGHT WEIGHT. I hear that "Cuban press" and push-ups w/plus (scapular retraction) work wonders also. Watch and learn: Shoulder Stabilizing Exercises - Reduce Injuries with innies and outies - YouTube

3) Listen to your body and be smart about your routine. Dumbell flies, reverse flies, pec dec.. these exercises may not be for you.

4) Spend several hours reading everything you can about shoulder function and prehab techniques. Read the rotator cuff horror stories too. It will motivate you to take care of your shoulders!

And, on a final note, it is my opinion that doing pull-ups and push ups every day is a bad idea. The shoulders already get hit with nearly every workout. When do you expect to recover? I understand the whole "greasing the groove" theory, but I don't think it's a good idea if you're already worried about your shoulder!!!