Majora's Mask is my favourite Zelda game, by far. The time thing doesn't matter. You are basically playing as Phil Connors in Groundhog Day. Skills/abilities you learn (songs, masks, etc.) carry forward (or rewind depending on your pov) with you to the next (or last) run through.
IIRC you can eventually unlock a song that skips forward (or back) to the start of the loop. Most of the quests will have a sort of soft checkpoint, where you learn a thing that allows you to pick up midway through. Once you get over the heebie-jeebies of being "on the clock" you realise time doesn't matter.