This is a footnote to John Winkelman's answer - please accept his answer rather than this one as he has correctly identified the anthology. Since I have the book I thought I'd provide some details.
The story is The Scalehunter's Beautiful Daughter by Lucius Shepard. I found it in the Fantasy Masterworks anthology simply called The Dragon Griaule. The girl who get's lost in the body of the dragon is the aforementioned daughter and is called Catherine. She kills a man called Key who raped her and flees into the dragon to escape the veangence of Key's brothers.
- A red plant that works as a stimulant and a blue plant that works as a depressant (might have the colors wrong)
I think you've misremembered this bit. The depressant, brianine, comes from pools of liquid and the sitimulant comes from a lichen:
From these liquids she derived a potent narcotic that she named brianine after her nemesis, and from a lichen growing on the outer surface of the lungs, she derived a powerful stimulant.
- A boy who initially provides her with much needed human comfort, but later becomes addicted to one of the aforementioned plants and stops being useful
Not a boy, but a man named John Colmacos who is injured his leg and becomes addicted to brianine after using it to help with the pain:
- Where the heart of the dragon is. She likes to listen to its strong, rhythmic beat
The story is basically a quest to find the dragon's heart, however the heart isn't beating:
Like one of those enormous Tibetan sculptures of the Buddha constructed within a tower only a trifle larger than the sculpture itself, Griaule's unbeating heart was a dimpled golden shape as vast as a cathedral and was enclosed within a chamber whose walls left a gap six feet wide around the organ.
- A ghost plant that can grow into the shape of a person and allow that person to reincarnate with a new body
This is the ghostvine. When Catherone first meets it the ghostvine has produced a copy of Catherine that claims to be her future self.
- A race of short, mentally-stunted humanoids living inside the dragon. She befriends them briefly before realizing that she can use them to escape the dragon and does so.
These are the Feelys. They are described as:
They’re most of them the descendants of a retarded man named Feely who wandered into the mouth almost a thousand years ago.