After the Red Year, much of Morrowind was laid to ruin. Did DIvayth Fyr perish, or simply relocate? Or is he still in the same place he was before? BONUS QUESTION: How exactly did he make "clones" of himself?

He's probably not dead.

Canonically, we don't know. It is more likely than not that he had a way of escaping and lives somewhere with his own personal "harem".

Magic mixed with genetics

I don't know, but he sure ain't here at the moment.

Also, flesh magicks.

I'd be surprised if he wasn't in Tel Fyr.

You know something? I kind of wouldn't mind Divayth Fyr being dead, because that would leave his legacy to being inherited by one of his four "daughters": Alfe, Beyte, Delte, and Uupse. While it doesn't require him being dead to do so, it would be cool to meet one of them in future games. And since they are all reputedly his clones, that would imply that they'll carry with them his magical gifts and brilliance.