Well, dips are fairly complicated movement for the shoulder, so it could be any of a lot of things that could be going wrong. Same with the L-pullups and such.
A vid of you doing them (dips and L pullups) would help clarify them a lot. Both the side angle and the back/front angle (with bare chest).
What you can be doing to help your shoulders obviously is rotator cuff work... mostly external + thoracic mobility and shoulder flexibility stuff. Ice and massage to the whole area to help alleviate any lingering inflammation and tightness.
That tends to clear up most stuff unless you have imbalances.