I'm no doctor by any means but have had shoulder problems on and off for quite a while and have learnt to try and analyse what's aggravating it rather than just looking for a fix.
Has the issue only been since you started cycling or were you cycling for many years without any problems before it started ... what happens if you take a break from cycling for a few weeks does it settle down or is it still bad ... if it settles down I'm not sure how much adjustment they made at your bike fit and if they believe it's now "perfect" or if you should really have a size smaller.
If it is the cycling that's causing it are you riding a drop bar bike, if so would you consider a flat bar bike rather than suffering the pain if it helped but meant you could continue cycling painfree.
I found 2 things really aggravate mine ....one is drumming and I haven't been able to find a way to stop it so have to severely limit how much I play and the other I believe is how I sleep on the shoulder and have changed where I put my right arm and always make sure I have adequate cushioning between the side of my head resting on my arm / shoulder when sleeping or try and avoid it altogether.
Many years ago I had an absolutely terrible wrist to the extent I was struggling to pick things up and couldn't work out what was causing it was for ages (nor could the doctors), eventually I realised I used to bend my hand over and put it under my chin / head when in bed / asleep and relax onto it applying pressure to bend it beyond it's natural stopping point ... the minute I worked it out it went away within 2 weeks ... it returned several years later but I realised I'd subconsciously gone back to my old sleeping habits ... As soon as I became conscious of this it went within days.