I agree - have at least three litterboxes.
Cats just do not get along with each other unless they are raised together.
I would think they will eventually tolerate each other, but your original cat will probably never be really happy with the other two cats there.
I believe male cats - neutered or not are always attracted to female cats. So that being said, your male cats will probably always somewhat harass your female cat.
It is amazing to hear that your cat was gone for so long and then came home. Someone must have taken her in. You ended up being stuck between a rock and a hard place now.
Cats just seem to act out by spraying. I guess I would try to maybe contain the males sometimes so the female gets a little freedom. Block the basement door maybe?
Keep us animal lovers updated....