In a surprising turn of events, it turns out Aki is actually the culprit! My big mistake was judging the birds based on their personalities as chicks, and not bothering to do a full investigation. (facepalm)
I recently checked the coop and found Bean, one of the hens, with a head injury. I spent awhile watching the birds and saw Aki chasing pretty much everyone around, attempting to peck at various birds' necks (including Mocha, my other rooster), and basically terrorizing the whole coop.
To see what would happen, I removed Aki, and suddenly the coop became a peaceful utopia. Nobody pecked at Bean's injury, even though it was bloody. They napped together and exhibited much less stressed-out behaviour.
Furthermore, seeing how lenient the hens (and Mocha) were towards Bean's injury, I put Pebble back in with them, and they pretty much acted like nothing had happened. They all napped together and ignored the injuries.
Then Basil escaped and disappeared into the neighbor's yard. That was stressful and I hope she comes back, but I'm not counting on it. I may invest in wing clipping.
Mocha seems to have had a complete 180 in personality since he was a chick. He used to be crazy, but now he's very sweet towards the hens and probably the gentlest rooster I've ever seen. Likewise, Aki used to be the chill one, but now he's showing quite a violent streak.
I'll observe more to make sure the injured hens are truly safe, and then Aki will probably be culled. I liked him cause of his pretty feathers, but I can't risk passing on his violent tendencies to new generations.
Any advice? I'm feeling very stupid right now for jumping to conclusions, haha.