Am experiencing similar issues. While I won't rule out a physical, age related impairment to the shoulder, I believe it's mostly related to tension in my case (usually starts after I've been practicing for 1.5 hrs or so). I try to stop as soon as I feel any pain and deliberately relax and or stop and do shoulder stretches before beginning again. Invariably I find that the pain is caused by tension which, when released, eases or eliminates the pain. Thus, I believe tuk's advice is well founded, even tho I haven't taken any Alexandre Technique classes personally. I have researched it and it makes good sense to me and so far, my DYI attempts at relaxation are yielding good results. Regarding the Giuliani (arpeggio) exercises, I've found that practicing them with open strings, right hand only, until I get them up to speed and then bringing the left hand into play for only the last few runs saves a lot of left hand (left shoulder) strain. They are, after all, right hand exercises. Per sphynx's advice, I am also switching to a 640 scale guitar, which I expect will also help.