Is my boyfriend over his ex?

Of course he liked her. I think he's telling you that, not necessarily as a lie, but more because he's either trying to spare your feelings or fend off a fight.

First off, forget what his pal said (actually, maybe be a bit pleased that he's not asking his friends to lie for him). And recognize your track record. You've been together for a significant length of time. If he was pining over her, you'd probably have seen that more clearly, by now. Absent clear indications of cheating, what you have is a guy who took a while to delete photos (but he did) and occasionally had a brain fart.

I suggest you do your best to not dwell on that, as it's counterproductive, and enjoy your relationship. Are you happy together? You wrote a lot but never actually mentioned anything about that. Consider that a lot more, and his brain fart a lot less.

PS My own mother has called me by my brother's name, more than once. I am female. People mess up details all the time. It does not mean they don't care. It means they just mess up a little. Is it malicious? Not from my mother, and it probably isn't from your fellow, either.