You can have a subtle injury to the support structure to the upper neck. An MRI will not usually show this. It could be that the radiologist does not have the skills to see the small difference or it could be that it falls within the range of a healthy neck.

An upper cervical specialist (NUCCA chiro, PT, DO, etc) may be able to find this injury. It is a slow injury to recover. It takes disciplined posture, especially during rest and sleep so the ligaments can heal and strengthen properly.

My upper neck took years of discipline to heal and is not fully healed. The injury has left me with some arthritis at C-0 to C-1 and C-1 to C-2.

Icing can help after an activity that causes symptoms.

You can also help yourself by learning a softer running gait. Try running with ear plugs in. You will hear your foot plant. Try to soften your foot plant so the sound is less. It might need a change of shoes plus a change in gait.

My best to you with this.