Hello~I hope you are feeling better by now, but if not, I would suggest seeing a chiropractor. You may have some misplace vertebrae and they are pinching nerves. He/she will take some x-rays and this will determine what area is the culprit, a few treatments and you should start to feel better.
I have had lots of acupuncture treatments, they never have had an adverse affect on me, I doubt very seriously if they caused the issue you had/ or are having.
Most likely the pain in your shoulder was coming from the cause of pain in your neck pinching one or more nerves going to the shoulder. Relieving the pain from that was easier than relieving it from the cause, which might be structural from discs impinging on nerves or it might be muscular. It will take a lot more help probably to solve the neck problem and you're noticing it more because you're not noticing the pinched nerve to the shoulder as much. Been there, done that, still doing that unfortunately.