The official chronological order of the series so far (and will be updated as time goes on). A very special thank you to Justice for confirming the order, and writing this amazing series. If any of y'all think of a categorization that'd make this look nicer, then drop me a line. And I hope y'all find this helpful when rereading the series.
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https://www.fimfiction.net/story/371250/bibliopocalypse-war-of-the-two-suns
https://www.fimfiction.net/story/349263/all-work-and-no-play
https://www.fimfiction.net/story/357415/fat-stacks-of-books

https://www.fimfiction.net/story/209600/cafeteria-control
https://www.fimfiction.net/story/406191/not-another-anon-a-miss-fic
https://www.fimfiction.net/story/220255/pinkie-and-sonatas-excellent-adventure

https://www.fimfiction.net/story/258808/together-we-can-name-this-town
https://www.fimfiction.net/story/350792/the-order-of-things
https://www.fimfiction.net/story/206382/stealing-the-deed

https://www.fimfiction.net/story/244260/the-dazzlings-are-insane
(Technically that one has no set timeframe. Since it's a mixture of stories in the life and times of the Dazzlings. Really worth reading. But happens throughout the MadVerse in the sidelines. Much like a Sidequel.)
https://www.fimfiction.net/story/359652/forward-always
https://www.fimfiction.net/story/222048/sonata-discovers-taco-town
https://www.fimfiction.net/story/260677/a-ban-domed

https://www.fimfiction.net/story/322092/sunset-shimmer-is-mad-about-everything

https://www.fimfiction.net/story/318186/tooth-hurty

https://www.fimfiction.net/story/346469/out-of-space

https://www.fimfiction.net/story/237397/a-dazzling-christmas

https://www.fimfiction.net/story/377428/breaking-out-to-avoid-being-broken-in

https://www.fimfiction.net/story/348586/a-newspaper-solves-everyponys-problem
https://www.fimfiction.net/story/370704/some-white-powder-solves-one-ponys-problems
https://www.fimfiction.net/story/371337/study-reveals-human-baby-flurry-heart-is-stupid

https://www.fimfiction.net/story/382818/aaaaaaaaaahhhhhhh
https://www.fimfiction.net/story/371890/mandatory-brunch
https://www.fimfiction.net/story/383230/spike-comes-to-his-senses

https://www.fimfiction.net/story/375949/home-again-home-again-jiggety-jig

https://www.fimfiction.net/story/412075/breaking-in-to-avoid-being-broken

https://www.fimfiction.net/story/422376/1/ununcommon-bond/in-hindsight-this-was-probably-inevitable

https://www.fimfiction.net/story/392063/the-beard-with-a-jerk-ass-hanging-off-of-it

https://www.fimfiction.net/story/429413/not-that-lonely

https://www.fimfiction.net/story/414415/daddy-issues
https://www.fimfiction.net/story/415122/sunset-shimmer-creamcorns-herself

https://www.fimfiction.net/story/417836/the-would-be-world-wreckers-club

https://www.fimfiction.net/story/419279/doggone-it

https://www.fimfiction.net/story/414796/1/black-magic/the-black-tar-heroin-of-the-coffee-world

https://www.fimfiction.net/story/425460/absolutely-abyssmal-afternoon (Doesn't have a set point in time in the canon timeline.)

https://www.fimfiction.net/story/431648/alicorn-allergy-season

https://www.fimfiction.net/story/435708/double-sunday

https://www.fimfiction.net/story/439348/the-benefits-of-friends