Another potential main antagonist could be a force from Harry's world that has followed him into the Kuroshitsuji crossover. This could be some sort of entity that doesn't want Harry interfering with the natural order of the Kuroshitsuji universe. It could be a being that has its own motives for keeping death and the afterlife in a certain state and sees Harry's actions as a threat, and so it actively tries to stop him.
Well, perhaps a concept is the power dynamics. If Harry is death in this crossover, he would likely have a great deal of power. In Kuroshitsuji, power is a major theme, especially with Sebastian's demonic powers. Harry's power as death could either clash or complement Sebastian's. This could lead to some really intense and unique storylines where the characters are forced to navigate around these two powerful forces.
Voldemort could be one of the main antagonists. He could follow the female Harry Potter through the portal to Middle - earth, causing chaos there. Also, the orcs and other dark creatures from Middle - earth like the Nazgûl could be antagonists. They would oppose the female Harry Potter and the hobbits or dwarves she teams up with.
Perhaps an ancient evil spirit that has a connection to death itself. This spirit sees Naruto as a threat because of his emerging powers related to death and tries to eliminate him before he becomes too powerful. The spirit could be using other villains as pawns to do its bidding.
The Volturi could be great antagonists. They might see the zombie outbreak as a threat to their vampire world order. They could try to wipe out all the zombies and anyone associated with them, including Bella if she has any connection to the zombies.
The Ministry of Magic could be the antagonists. Since Harry is in a gang, they might see him as a threat to the order of the wizarding world. They could send Aurors after him and his gang mates, trying to arrest them and break up the gang.
It could be Voldemort still. Even if Harry and Hermione are sent back in time, Voldemort would still be a major threat. His dark magic and his followers could oppose Harry and Hermione's attempts to change things.
One possible antagonist could be a rogue ninja who also wants the power of the Rinnegan. He might see Naruto as a target to either steal the power from or eliminate so that he can be the most powerful in the ninja world. This character could be a new creation or an existing villain with a new motivation.
In the RWBY world, Salem could be a major antagonist. She might view Naruto's son as a threat to her plans for Remnant. His unique powers and knowledge from the ninja world could potentially disrupt her schemes, so she would try to eliminate him.
There could be a new type of hybrid creature that is a result of the combination of the zombie virus and some supernatural element from Bella's world. This hybrid could be extremely powerful and unpredictable, and it sees both humans and zombies as a source of food or something to dominate, making it a very dangerous antagonist in the fanfiction.
The Thalmor could be great antagonists. Their strict control over magic and their anti - human beliefs could put them at odds with Harry. They might see his different form of magic as a threat to their power in Skyrim.