cherry-picked explanations

quarry: area below the rock farm (or the rock farm itself)
accent changes: igneous and cloudy’s from the cutie mark chronicles to hearthbreakers, limestone and maud’s from hearthbreakers to best gift ever
acacia, oak, spruce, birch pie: pinkie’s cousins
obsidian pie: fanon character in the muffins saga & fanon name given to maud pie (along with clyde) after her appearance in pinkie pride
marble pie dialogue: comics and a book
pinkie calling her sisters “the sisters”: implies they aren’t her sisters
marble scrapped in the ending of the end: here
addressing each other by full name: either by entire name (pinkamena diane pie) or with their last name included (“slow down, pinkie pie” “buck up, pinkie pie” “earlier today, limestone pie..”)
pie sisters based on temperaments: phlegmatic, melancholic, sanguine, choleric
maud’s journal: seen in comics, features rarity, insight into maud’s mind
magic duel: rock farm seen in trixie’s flashback
maud narrow’s eyes when angry: before groaning at pinkie in s7 ep 4, when pinkie does an impression of her in s7 ep4
rusty tenure: seen beside maud pie getting her rocktorate in s7 ep 4, coat color matches igneous and eye color matches limestone
pinkie is adopted: li’l cheese does not resemble pinkie’s parents or any of her sisters, only her
buried treasure: nemesis of maud pie in comics
marble pie talking at the end of hearthbreakers: not audible
marble pie singing in best gift ever: here

stygian: multicolored mane like marble pie, similar coat color
pizza pie: april fool’s version of pinkie pie that is technically canon in some timezones as they are outside of april 1st
pie family are crystal ponies: theory that i forgot the reason for, similar multicolored manes, dull colors, attachment to gems/rocks, maud shares eyelash design with crystal ponies
octavia melody: eye color similar to marble’s, grey coat similar to maud’s, earth pony
rockville: name given to the rock farm, implied town
star swirl: resembles stygian
boulder is the pairing stone: boulder communicates with maud pie
limestone in marble sense: implied by maud & pinkie sense
igneous is a step-dad: none of the pie sisters resemble him
poster in starlight’s old room: near top left
pie sisters born in manehattan: limestone and maud switch to a manehattan accent in best gift ever
between dark and dawn: igneous pictured left
rarity and limestone: here
maudbriar is incest: mudbriar resembles pinkie’s cousins
blue-eyed limestone was actually maud: filly limestone here has the same eye mane and eye color as filly maud, meaning maud existed all the way back in season 1 yet was removed (a third sister was also implied here), and if it was maud and marble entering the house, that implies limestone stayed outside, therefore limestone was the designated workhorse from the start
pie sisters hate gummy: see marble’s eyebrows and maud’s eyes
limestone says “i love this, it’s so great, yeah” at the end of hearthbreakers: here

pinkie & maud have chaos magic: pinkie is able to predict the future & maud can teleport
maud told limestone about mudbriar before pinkie: limestone already knew who mudbriar was despite living away from ponyville, implies maud travelled back to rock farm, implies distrust of pinkie
discord: discord resembles stygian and mudbriar, pinkie is able to change shape, teleport, and float without a horn
maud & pinkie are delusional: maud implies she believes a rock talks and states “im very funny”, yet ponies only laugh when pinkie comes around, pinkie pie has episodes of psychosis/delusion (party of one, accusations in mmmystery on the friendship express, potentially her side in ppov, starting to believe the mane six as opposites in the maud couple (“i never learned to read”), believing that rainbow dash is evil pie hater dash, potentially entirety of pony life which explains sugarcube corner being the main location)
starlight glimmer: multicolored mane, similar coat to pinkie pie, magical, poster on wall
maud is sweetie drop’s coworker: able to destroy a giant rock by punching it (replace the rock with a bugbear), mysterious like sweetie drops
blinkie is hoity toity: here
cheesepie is incest: cheese sandwich resembles mudbriar and igneous and is an earth pony

limestone can see the future: potentially knew about holder’s boulder falling, knew that applejack changed her farm before even going outside
maud is a changeling: maud pie is detached in seasons 4-7 and doting in seasons 8-9, temporarily disappears in the maud couple before personality changes, also this and maud not appearing until season 4, maud has been a changeling since the start and feeds off pinkie’s (and mudbriar’s) love rather than working on the farm
maud died in s8 ep3: disappeared before having a personality change
limestone killed the real maud in s8 ep3: explanation for awkward moment in same episode
maud is suicidal: maud gets eaten by a quarray eel and doesn’t care, wants to “turn into a rock” (think rockhoof or discord or cockatrice), noticeable lack of enthusiasm before disappearing in the maud couple
maud pie’s cutie mark represents mind control: tom hypnotized rarity, boulder “communicates” to maud, choosing stone, reverence to holder’s boulder, pinkie’s “friend group” including rocky, a stack of rocks, starlight says that she and maud “just got each other”, pinkie perceives more emotion from maud, scares rarity & street rat just by looking at them
holder’s boulder mind controls the family: says the boulder gives them good luck despite living in terrible conditions, slaves away at rocks all day just to eat rocks for dinner, and applejack unluckily plants a flag on a fault line which unluckily causes the boulder to fall into the quarry
holder’s boulder gave chaos magic to the pie family: explanation for good luck

corrections
limestone is the oldest: here
boulder is the pairing stone: boulder is actually the choosing stone, my new theory is that the pairing stone and the choosing stone are different, the pairing stone selects pairings while the choosing stone reasons not to, boulder is selective (calling jewelry “stuck up”), this implies that there is another boulder, or that the pairing stone is actually holder’s boulder (the teams in hearthbreakers were paired in the presence of holder’s boulder, and the apples and pies reunited in the presence of holder’s boulder)

not added to chart
pie sister names based on pie (theory): key lime pie, marble pie, mud pie
clyde & sue: fanon names given to igneous (and maud) & cloudy
marble pie eyeshadow: marble wears eyeshadow like maud here, doesnt wear it before or after
mentally retarded maud fanon: popular fanon between pinkie pride (maud’s first appearance) and maud pie’s episode is that maud (named clyde jr. then) was mentally retarded
the ghost of obsidian pie: memes of maud (obsidian) appearing in photos because of maud suddenly appearing in pinkie pride despite not appearing in the original scene
limestone pie’s cutie mark/talent (theory): limestone pie is a sculptor and her cutie mark represents adding “flavor” to rock, which means she appreciates the beauty in rocks (like a geode) even if she doesnt understand some art
nick confalone hearthbreakers notes: here and here
pie family could’ve been pegasi: 2008 g4 pinkie pie, may or may not imply that mudbriar, cheese sandwich, and li’l cheese are pegasi as well
mince meat pie & chicken pot pie: here
pie in the sky: this april fools tweet by meghan mccarthy states that season 4 episode 14 was going to be called “pie in the sky”
marble pie’s inconsistent mane design: here
the maud couple storyboard: here
the cutie map storyboard: here
best gift ever storyboard: here
no talking, no smiling, only rocks represents the pie sisters (theory): no talking = marble, no smiling = maud, only rocks = limestone
pie family knows apple family (theory): granny smith asked if the choosing stone knew some “apple-farming hunks” and igneous said “indeed so”, or the choosing stone itself is just omniscient, also igneous knows granny smith’s name before she introduces herself
pie sisters origin: here, implies limestone’s personality was predetermined, unknown 4th pie sister
maud’s dark and stormy night: maud mentions that she met boulder on a dark and stormy night that changed her life forever, could potentially be the reason the pie sisters changed
pie sisters became the way they are because pinkie moved out and/or octavio pie died/moved out: pinkie pie lost her yovidaphone and nearly turned monochrome, now imagine the pie sisters losing a family member (or 2)
holder’s boulder is a benevolent god (theory): if holder’s boulder is the pairing stone, holder’s boulder forgave the apple family and convinced the pie family to reunite (even maud was displeased, then was convinced)