I'm not pregnant, but had a baby 15 months ago, I had an episiotomy and some tearing. Then I ended up with bloodclots and burst stitches, all this took quite a while to heal and even now feels tender, particularly during my period when its uncomfortable. I've always assumed it's due to hormonal changes & increased blood flow, which, if I'm right could explain why you're having pains too.
Mention it to your MW, maybe she can explain it?! Hope you don't suffer too much