I would still get the pain checked out, make sure there is not something wrong now; would be a shame to find later that the pain was from now, even if the memories were not. Just tell the doctor about the pain, not what you think it may be from, see if s/he can find something. If they ask, do tell them you were abused but don't go into detail, just say you would rather not talk about it.

There could be scars or any number of problems that could have gotten worse as you have grown/matured and be just now presenting themselves since you are working on your abuse in therapy. They don't have to be "phantom" just because you are working on the past; thoughts and memories may wander around in our heads and be suppressed, etc. but our actual body has a mind of its own :-)

I hope you feel better soon.