I agree with your diagnosis, there is still something in there. My son had a piece of wood in his foot for some time, and when he finally went to the doctor, he dug it out but it still hurt. Two days later, my son squeezed it and a second, bigger piece came out enough to grab it with the pliers.
...and yes, they hurt all out of proportion to their size. I had one hurt so much that I stopped carrying stuff in my right pocket until it worked its way out enough to get hold of it, because it hurt to put my hand in my pocket.
Anyhow, glad you got part of it out. Here's hoping the rest is evicted soon.