Does anyone have that story anymore?
I hope so. I mean this in the most polite way but it seems fairly unpersuasive to say that, as so many matters of lore come down to twists of specific wording. Subjects are hardly settled without the wording in front of us. ;D

Babaganoosh has taken pains to describe all the non-human races. Just look at the ever present Yordle Vs Meggling business. If Yi is a member of a whole race of multi-eyed mutants, it really seems like someone wouldve mentioned it by now.
"When the armies of Noxus invaded Ionia, Master Yi joined in the Ionian defense to fight the craven enemy, bringing his village honor through his unparalleled mastery of the blade."
"Master Yi now brings his mastery of the blade to the League of Legends with unflinching purpose: to avenge his kinfolk and end the predations of the Noxus once and for all."
His background paints his kinfolk as Ionians. Who will declare Ionians have [x] eyeballs?

And hey, I'll add another unpersuasive thing: The matter of Jax's fingers 'n toes has come up more than once before the lore forums. There was talk of his gloves meaning nothing because his fingers could be distributed in them. If ever there was a time to put it all to rest, its now. Lay out the Noosh bait once more!

Fantastic! Thank you very much for that. Even if its no longer so very official, its still fascinating and your effort improved my day. A thousand years old and folding space itself? When they named it 'League of Legends' back then, they mustve really meant Legends..

We see a lot of his story elements Have carried over, and I find it extremely likely he simply went from ancient being to very gifted human, not very gifted Ionian Beholder.