It sounds like you recieved a pretty good adjustment. The trap is going to get envolved with a good cervical adjustment. Take about 48 hours for that to clear out. Has to do with repositioniong the head back above the shoulders. Of course the trap has to readapt to "nornal" and sometimes that makes it ache a bit. But again, not for very long.
What I advise against is the sudden rotational manipulation of the head and neck some guys use just to hear the bones crack. Anyone can do that.
Of course there will be some noise with a good adjustment. The bones will make that cracking sound. So from what you're saying even though the trap ached for a couple of days it sounds like the guy did a good job. It's not that uncommon the hear from folks. "Doc, you made my shoulders hurt". About 48 hours it's gone.