Yakitsuki was Pregnant and Aborted
In the world with fetus and umbilical cords, there are a lot of needles, which are used in illegal abortions. In addition, the event with the big doll shows it emptying of blood and more particularly of the belly. The atmosphere of the game is generally calm, with many shades of white meaning that Yakitsuki is depressed and does not assume her act.
Yakitsuki is a Photographer
One effect that Yakitsuki can get is a camera that lets her take photos. There is also a board in her room that fills with photos as she collects effects. Both of these things suggest an interest in photography.
Nature could be Yakitsuki's subject of choice when photographing, as the Camera effect is found in a burnt down forest, as well as a number of the dream areas (Clover World, Dark Mushroom Forest, Wilderness, etc) and effects (Mushroom, Flower Vase) are related to plants/nature.
Yakitsuki's House was Burned
From the Burned Ground we know that it's possible Yakitsuki had a tragedy of losing her house, camera and important people in a breaking out of fire. It might cause by an accident from the microwave which Yakitsuki can find the Microwave effect in the Snow World, considered it connected with Burned Ground.
The Date of The Accident
In the Electronic Tube World, you can find some numbers on the electronic tubes, two of the combining numbers are "2004 06 26" and "12:59:58(9)", possible hinting something happened to Yakitsuki at 12:59 am of June 26, 2004. Since you can find the Snail effect here, it might mean Yakitsuki wanted the rain to extinguish the fire at that time.
Although the numbers "2004 06 26" are probably just a reference to when Yume Nikki was first released.
Yakitsuki has a Congenital Disease
It’s possible that Yakitsuki has some sort of chronic illness gained at birth that makes her fatigued easily. Withers features a LOT of medical motifs and fetuses. She may have spent a lot of time in the hospital as a kid, which gave her trauma. The weapon is a drip stand for crying out loud. Both of the faster movement speed effects take Yakitsuki off her feet. The wings lift her up and off the ground. The wheelchair speaks for itself. It’s possible that walking is tiring for her, so she moves faster in her dreams when she’s NOT walking. This would also explain why she’s a shut in. If she’s ill and constantly fatigued, it makes sense she stays in her room and explores dreams instead. Even the NAME Withers could tie into this idea -- almost as if she’s withering away from illness.
These other connections are a bit more of a reach, but I’ll throw them here anyways. The camera effect and photo board could reflect that since she doesn’t get outside much because of her condition, she likes to take photos to cherish the memories she does have. The vase effect could be a reference to flowers that people sometimes give to loved ones in hospitals. The guinea pig effect could possibly relate to how she may have had experimental cures tried on her.