As for the overall goals:

Maintain the ‘Nobodies’ Theme: Consistently depict Rey’s parents as ordinary individuals (“nobodies”) throughout the background story, reinforcing TLJ’s theme that greatness and significance in people can emerge from humble beginnings.
Deepen Rey’s Character Complexity: Provide Rey with a more complex and nuanced origin story that includes a more direct genetic link to Emperor Palpatine, creating internal conflict and exploring themes of identity and destiny due to the sinister reason behind her existence as a person (to be a vessel).
Emphasize Personal Choice and Agency: Rey’s adoptive parents are able to make the correct choice in the end despite being involved with the wrong crowd - similar to Vader. Also, highlight that despite her origins, Rey’s choices and actions define her, aligning with the overarching message that individuals shape their own destiny.
Explore Nature vs. Nurture: By making Rey a clone/genetically derived from Palpatine, the story delves into the debate of nature versus nurture in twins, questioning whether one’s genetic makeup or upbringing plays a more significant role in defining their path.
Strengthen the Emotional Narrative: Enhance the emotional depth of the story by detailing the sacrifices and struggles of Rey’s adoptive parents, adding a layer of tragedy and human emotion to her backstory - instead of being mere plot devices.
Align with Established Canon: While introducing new elements, ensure that the revised backstory remains coherent with as much of the established Star Wars universe as possible, respecting its lore and thematic essence.

This is where I’m at with the story itself, formatted as dialogue a few posts above. I don’t see anything particularly wrong with any of it.

Rey’s Parental Background:

Rey’s parents are depicted as ordinary, unremarkable individuals throughout.
As nobodies, they are easily lured into the Sith cult because they want to find some sort of purpose in life.

Rey’s Origin:

Rey’s parents were assigned an infant (Codename: Rey) by cultists from Exegol.
However, when Palpatine orders the termination of his clones, they want out of the cult.

Parents’ Sacrifice:

Rey’s parents have grown to love her, finding their purpose in life, and decide to hide her from Palpatine.
They leave her with Unkar Plutt for her safety, paying for her protection instead of selling her (Kylo misinterpreted the currency exchange direction).

Parents’ Demise:

Seeking further help, they look for Luke Skywalker’s allies in the Jakku desert.
Palpatine’s assassins eventually find them.
Rey’s parents resist but are ultimately killed, their story forgotten by the galaxy.
Ochi takes their Sith ship for his own most likely because he wants Rey to recognize it and be drawn to it.

Palpatine’s Motivation:

Palpatine sees his clones as unnecessary and a threat after his return, leading to the order for Rey’s termination.
Rey is revealed to be a clone experiment based off of Palpatine’s genetic template to prevent confusion.

Rey and Kylo Ren as a Dyad:

Kylo Ren reveals they’ve become a Dyad in the Force, a powerful and rare connection.
Subtly imply that the power is so strong that Palpatine cannot use his foresight to be made aware of it
He proposes using this power to end Palpatine and the Sith, and to create a new path together.