One great 'trans pokemon fanfic' is 'A Trans Trainer's Journey'. It has an interesting plot where the trainer's transgender identity adds a unique layer to the story, like how they interact with different pokemon types in a new way. Another one could be 'Transformed in the Pokemon World' which focuses on a character who undergoes a transformation in the pokemon world while dealing with their trans identity. There's also 'The Trans Pokemon Trainer's Adventure' that has exciting battles and a great exploration of the trainer's self - discovery within the pokemon universe.
First, create your main trans character. Decide on their backstory, like how they discovered their identity. Then, think about how this identity will interact with the pokemon world. For example, maybe they have a special bond with a certain pokemon because of their shared sense of being different. Next, plan out the plot. It could involve a pokemon journey where the character also discovers more about themselves. Don't forget to add details about the pokemon battles and the different regions they visit.
There was a recommended novel about transmigrating cells and cultivating immortality called "Cell Cultivation". This novel was a Xianxia/Cultivation novel, which included transmigration, prehistoric, interstellar, and technological cultivation elements. You can read this novel on Qidian Chinese website. The author is China's Jiao Zi, Giant Panda.