Firstly I'd stretch your rhomboids, traps, shoulders in general every morning and whenever you have the chance to do so as this will loosen them up and aid recovery. Then get some massage (it can be expensive thats the only isue - suppose depends on where u live in the world)!
Then i would try and strengthen the shoulder cavity / rotator cuff muscles themselves. They may be inflammed or damaged from heavy lifting, technique issues, lack of rest, poor posture, sitting at your desk all day at work with a slumped position, the list goes on. Avoid lifting heavy with the shoulders and go to a physio and ask them for the green theraband i think its called - its a stretchy band that you can tie to a door handle and perform various rotator cuff rehab movements with.
Another one - stand near a wall, place your hand on the wall with your arm extended fully above your head, keeping your hand on the wall lean your weight into your arm until u feel it in your shoulder and this will work as a recovery exercise as well. You can find plenty of shoulder rehab routines on you tube.
Do you suffer from tension? I did years ago and we all do sometimes - the tension from your traps will spread all the way from your shoulder right up into your neck where it connects to the skull! its a right old pain!!
MASSAGE, STRETCHING, SHOULDER / RHOMBOID / ROTATOR CUFF rehab exercises - textbook causes of your symptoms.
Cheers and hope it gets better.