Two cords aren't missable.
Third cord:
1. Send whore to chapel.
2a. If you want to use her blood: kill nun in gaol, send nun to clinic, or send nun to chapel, get her gesture, and then kill her.
2b. If you want to use nun blood: send nun to chapel, take her blood ONLY, play game normally until you kill Rom. At that point blood is no longer available and as long as the whore is still alive she should stay that way.
3. Complete Nightmare of Memsis and finish the whore's story stuff to get the cord.
Alternate third cord: Don't mess with Iosefka (meaning stay out of her room when using rear entrance, it's ok to loot the rest of the clinic) until after Rom is dead. You lose out on a rune doing this, however. Pretty useful one if you like parrying, but there's a superior version in chalice dungeons.