Shoulder Pain

Both of my shoulder joints were bothering me when I woke up.  I warmed up my shoulders with some mobility drills, front raises, lateral raises, the one where you stand against the wall with your arms on the wall and extend them at a 45 degree angle.  

I did my normal lifts, squats, bench press, deadlifts, bent over rows. In between my squats and bench press, I did more mobility drills, I benched 3x5x115, and afterwords I stretched my shoulders.  My right shoulder now feels fine, but there's a little muscle pain in my left shoulder when my arm is at or near 90 degrees, especially if it's in an upright row position.  Lifting my arm a little bit is fine and once it's past 90 degrees it feels fine.

For now, I'm icing it and taking it easy.  Is there anything else I should be doing?

My shoulder book, and my physical therapist, both say not to do lateral raises. Front raises are OK though. 

I remember seeing upright rows in some your past workouts. You may? want to go with something else on that one. I've seen recommendations against that, but I think the danger might have been more for the elbow (the lateral tendon gets inflamed).