So I've realized that the LPS: Popular Episodes don't really fit in the same timelines, so i thought that there are probably different chronologies.
From what I've seen is that there are these timelines:
SEASON 1s
[Official] Season 1 - Includes Who's That Girl? - Pretty Face, Ugly Heart (By sophiegtv)
[4 Friends] Season 1 - Includes Basically Twins - No No NO! (By ChillyCookie5)
[AbbavsKnight] Season 1 - Includes The Start (By PetLoverGirl)
[MySchoolLife] Season 1 - Includes Mia's New Life - Best Friends For Never (By EmilyLuvsLPS)
SEASON 2s
[Official] Season 2 - Includes Savannah - ??? (By sophiegtv)
[Fan-made] Season 2 - Includes Savannah's New Life - Stupidity and Madness (Varied)
[Fan-madeAlt] Season 2 - Includes Savannah's New Life - Should I be Friends with you? (Varied)
[Fan-madeAlt2] Season 2 - Includes Savannah's New Life - Morley Glory (Varied)
[Fan-madeAlt3] Season 2 - Includes Savannah's New Life - No One Likes Video Games Silly! (Varied)
SEASON 3s
[Fan-made] Season 3 - Includes Brooke Team - Being Elite is Sweet (Varied)
[Cousins] Season 3 - Includes Savvy's Cousin - Real Me (By PetLoverGirl)
[Prom] Season 3 - Includes Savvy's Cousin - The Prom - Being Elite is Sweet (Varied)
Read the chronology in a bit more depth here: Episode Chronology (wip)
Wow that took a while. Any questions or corrections, just pm me or whatever.