It could be Orochimaru. Since Orochimaru has a long - standing feud with Jiraiya and is always up to no good. If Naruto ditches Jiraiya, Orochimaru might see this as an opportunity to manipulate Naruto. He could try to convince Naruto that Jiraiya was holding him back and that he can offer Naruto more power, all while having his own evil plans for Naruto.
No, Boruto is alive in the manga. The plot hasn't led to his death. However, the manga is ongoing, and anything could happen in the later developments.
There may be some interesting Kushina and Jiraiya fanfictions. You could search on platforms like Archive of Our Own or FanFiction.net. When looking, pay attention to the tags and summaries to find ones that focus on the elements you're interested in, such as their friendship or potential collaborations in the story.
One great fanfic could be about their adventures before Naruto was born. It might explore their relationship dynamics, how they trained together and supported each other. Maybe in this fanfic, Jiraiya tries to convince Tsunade to take on more dangerous missions with him, showing his trust in her abilities.
It could lead to Naruto becoming even stronger and more skilled than in the original story. Jiraiya's training methods might unlock new powers for him.