robinauts

"Kurogane scoffed, but settled down as Fai took a swab, dabbed it in the calendula and chamomile wax, and spread it on the bite marks."
The Calendula flower can be used to heal bite marks and lacerations. Chamomile means love and purification, and can remove curses cast against you.

“'You can bake if you want,' Kurogane commented, flicking a stray daffodil petal at Mokona."
Daffodils stand for uncertainty, chivalry, respect, "return my affection," and new beginnings.

"Stop throwing grass on me!"
...grass symbolizes homosexual love.

"Afterwards, they had gone out to dinner - at 'The Granny’s Bonnet,' Subaru recalled."
Granny's bonnet is another name for the aquilegia or columbine flower. It stands for deceived lovers, ingratitude, and faithlessness.

"[Syaoran] then went over to Sakura, who put him to work dicing lilac stems."
Lilacs are symbolic of the first emotion of love, youthful innocence, and memories.

"Fai fetched some dried marigold from the potion pantry..."
Marigold is used for visionary sight and finding stolen/lost property.

"'You’re the one who helped the Almira pod out with that lusca last summer!'"
Almira is a small town in Washington. A lusca is a sea cryptid/monster/globster; it is apparently half shark and half octopus.

"'Daylight’s not exactly in short supply around here, booboo-bear,' Fai cooed, deftly snatching his hat and ducking from Kurogane’s swat in one move."
I am obligated to tell you that 'booboo-bear' is a gem from the treasure trove that is this Yahoo Answers page. Watch this video for max hilarity.

"The Interior August Offices were concealed from the main floor by two polished alder doors..."
The alder is the "tree of fire." It also has the properties of concealment, protection, and the bridging between worlds.

"...he’s narrowed it down to either a kulshedra or a phoenix.”
A kulshedra is a monster from Albanian folklore. It starts its life as a bolla which sleeps all year, only awaking on St. George's Day, where it eats a human then goes back to sleep. When it's twelve years old, the kulshedra grows a lot more appendages and causes droughts until it receives sufficient human sacrifices.
A phoenix is a fire bird that can resurrect itself by burning itself to ashes. This is a bit more well-known, so I won't go into detail.
Remember that I'm playing a bit fast and loose with mythology!

"Aquarius above, what an awkward pause."
Aquarius is the constellation of Ganymede, Jupiter's cup-bearer and young lover. He's used a lot as a sign of male homoeroticism. (My original intention here was to have Fai say whatever the planet that symbolized gayness was, but that turned out to be Uranus and that was a little too on-the-nose for me.) (Although Aquarius is the patron constellation of Uranus, so I guess it all works out.)

"...grabbing a small glass bauble and a few ingredients - marigold, aloe extract, thistle."
Marigold aid with finding lost items and giving visionary sight. Aloe gives protection against evil influences. Thistle gives protection and aids in hex breaking.

"'Sakura, please get me the eucalyptus ink from my study...'"
Eucalyptus grants protection.

"...Fai got out a tin of dried vetivert; he then bundled the hair in the twigs and stuck it in the bauble."
Vetivert protects against theft and aids in hex breaking.

"...his cedar wand..."
Cedar helps clear away negativity and is generally cleansing.

 "'Do you want raspberries on your pancakes?'"
Raspberries signify protection and love, and could conceivably be harvested in November, when the story takes place.

"...pouring the residual magic from his dreams into the chunk of amethyst that shined by the window..."
Amethysts in general have a whole good for spiritual meditation thing going for them. They're a very important crystal in modern witchery.

“'Please make sure to take some labradorite with you today.'”
Labradorite is a crystal that heals and protects one's aura.

"...he had been going to visit his plot at the community garden, expecting some tomatoes and sage..."
Sage is used to banish negative spirits and grants protection, wisdom, wishes, immortality, longevity, etc - used a lot in witchcraft. Tomatoes could conceivably be harvested in April.

"A little old woman with bright yellow eyes toddled out."
This isn't anyone specific and it doesn't really matter, but I have obaa-chan from xxxholic in mind for this role.

"'I’ve heard a few people talking about hoop snakes making nests in parks on the forest side, and the calls of a strix at night...'"
Hoop snakes are a mythological creature/cryptid from the US, Canada, and Australia. They're kind of similar to the Greek ouroboros, as it's a snake eating its tail - but a hoop snake takes that to the next level. It rolls really fast at someone and then bites it. A strix is an owl that eats human flesh, from Greek mythology.
 

I would also like to say that my decision to make Fai not cis was based on personal headcanon. There are some unfortunate sections of wicca/paganism that are obsessed with menstruation and moons and whatnot. That is not the case in this fic - being a witch is a gender neutral profession. Later on in the fic, cis male witches will appear. The matter of Fai's gender or body will not be used as a plot point.
You can view him as a trans man or non binary in this fic as you prefer; all I know is that he's not a girl but still enjoys feminine fashion. I view him as having "less of a gender than an aesthetic."