Hi Joel,
I'm surprised you didn't have the ache sooner! My neck muscles on the side of my dissection (some turkey neck going on for sure) as well as shoulder muscles, the muscles of my upper back and my entire body for that matter ache! ~lol~
Depending on where you are in recovery there could be many reasons, nerve regeneration being one of them. Also, we tend to compensate (posture, movements etc.) for deficiencies and and that can cause muscle ache.
"T"