I've been battling the same for a while now and have reduced its frequency and duration, though I suspect I am going to have to take the plunge and get some physio work done to see if that will help further.
I have managed the discomfort through the following:
- Change from two pillows to one, or none at all.
- Adjusted my driving position in a major way, so not reaching as far.
- Changed my position when cycling, so handlebars are closer.
- Strengthened my upper back muscles through 'butterflies', etc
- Stopped carrying heavy things on one side only.
- Taken magnesium daily.
- Applied Atrogel (Arnica) and taken Arnica tablets after aggravating the symptoms.
- Try to avoid caffeine and stress.
Like you, I exercise a great deal and most important was being able to continue that.
However, I have switched to higher intensity, shorter and more varied forms.
I can't claim to have entirely remedied the problem, as I drive long distances every week and have a bad habit of working at a tablet on my lap, so my neck is straining downwards to glance at it but I know what the triggers are now and have made those adjustments.
I have a very slight scoliosis (curvature) of the upper spine that is likely to be the cause of my muscular pain.
All will have this by older age but some develop it a little earlier, so it may be worth seeking a free introductory consultation from a physio.
If they confirm that or a similar mechanical cause, then supplements are unlikely to reverse the cause but targeting the affected muscles will help.
I'd strongly suspect the cause is mechanical but since it comes and goes and you can identify activities that aggravate it, I'd not worry about it causing other problems, or having a serious underlying cause.
Rarely, a tumour in the spine can lead to pain but this is very rare and would affect your co-ordination and circulation to the limbs.
Far far more likely, though, the cause is as discussed.
If you search for "neck headaches" you may find the symptoms you describe.
And yes, you should find the problem resolves a couple of weeks after it came on (unlike mine)..