Are carried over Personas allowed to be used on the save since its NG+? What does it mean by Timer stops at NG+ save? By True Ending does it mean maxing all Social Links or just beating Nyx?

I would assume personas are allowed, but someone else ought to verify. Timer stops at NG+ save means that you stop the time when saving your file after having watched the end credits. True ending just means beating Nyx.

Awesome thanks for the answers.

Got one more question now, does the 'timer start at power on' mean when you turn on the console/emulator?

Yes, or if using a PS3 it starts when you select the game on the main console menu.

This game wasn't released for Playstation 3, its vanilla Persona 3.

There ¤are¤ backwards compatible PS3s. They're normally banned for speedrunning, but MLSTRM isn't technically wrong.