This has no connection to Xenophillia but was inspired by Divided Rainbow by Mike Teevee, a much better side story. In particular, he pointed out that there were (1x2x3x4x5x6) = 720 possible ways the Mane 6 could have been scrambled. He also had the Elements altering history (or at least, Ponies memories of it) to account for the fact that nobody except Twilight was freaked out by the shift.

This is one of the 120 possibilities with Pinkie as Element of Magic

I know where I want to go with this story, but not sure "How to get from Here to There?", so I am putting this on Hiatus .

All The Myriad Ways (Niven)

for a hint.