Sounds like you have impingement. The worst thing you could do right now is any overhead pressing motions, also bench and incline probably bother you. For weight training, eliminate any overhead pressing for the time being and change the incline and bench to DB with neutral grip (palms facing each other). This position allows an increase in subacromial space that is lost with a barbell. Concentrate on rowing motions motions and you could also try pulldown motions with a close, supinated grip which helps to open the subacromial space.
What you would want to concentrate on is stretching your pectoral group and your shoulder external rotators (teres minor and infraspinatus) which when tight cause an anterior shift of the glenohumeral joint which decreases subacromial joint space causing impingement and ultimately rotator cuff tear/surgery if left unaddressed.
The pectoral group is easily stretched in a door way with 3 positions...
1) forearms flush with door frame, elbows at 90 degrees, 90 degrees under arm
2) straight arms/elbows reaching toward corners of doorframe
3) straight arms/elbows reaching overhead to top of door frame (unless this position bothers you)..repeat each for 30 seconds numerous times throughout the day.
To stretch the external rotators you could use NEER functional IR stretch which involves using a towel/belt/rope over your good shoulder and putting the involved arm behind the back and pulling up with the opposite arm/towel. Be sure to maintain scapular retraction so that the shoulders don't wing resulting in a loss of the stretch.
Also you could use a side-lying sleeper postion stretch (if you can tolerate lying on the shoulder). This position is preferable due to the stabilization of the scapula against a hard surface which transfers the stretch to exactly where you want it. http://www.epicenterperformance.com/uploads/documents/PurePower-Shoulder.pdf#search='sleeper%20stretch'
some other good stretches to perform here also
Another contributing factor to impingement is posture, make sure you are sitting up properly without your shoulders rounded forward or head forward. This improper posture causes muscular contractures that result in anterior translation of the humeral head resulting in decreased subacromial space causing impingement.
As far as strengthening of the cuff is concerned, concentrate on external rotation movements (outlined in several articles on T-Nation). Including sidelying external rotation with light weight and TheraBand standing external rotation (you probably did this previously in PT). Also, concentrate on proper strengthening of the posterior musculature/scapular retractors.