Okay, to ease your pain, here's some MM pointers.
1. Play the song of slow time. It slows time down to a crawl. It is the opposite of the song of double time, which helps you skip a day.
Songs to know:
Song of Time
Inverted Song of Time - this slows down time.
Song of Double Time - this allows you to advance time.

When starting on day one, always play the song of inverted time immediately. It will slow it to a crawl, and you will have a shit load of time to do what you want.
See them in action here:
2. Replenshing rupees, bombs;etc.
Before going back in time, if you have a lot of rupees, go to the bank in Clock Town. Deposit your money, then play the song of time. More than that, when you get the Goron mask, you will be able to replenish rupees, bombs, and more easily by going out into Termina field and doing this.
0:00 - 0:12
3. When you unlock a dungeon, just save and go back to day one. You will have the ability to go back since you'll still have those skills. Then play song of inverted and quick travel to the dungeon of your choosing. Each dungeon I think has a mid-boss or something that also allows unlocks a quick thing that allows you to skip to the mid point of the dungeon. So if you're on day three in the middle of a dungeon, save and quit and utilize this. You'll be able to start at the halfway point. Fantastic dungeon design. Of course, with song of inverted, you usually have enough time to clear the entire dungeon before getting a game over. You have that much time on your clock to do it.
The reason why the puzzles in the first dungeon were amazing is because a very simple thing that Majora's Mask does that no other Zelda does: pre-dungeon puzzles. Usually, in Zelda, you gain the item you need IN the dungeon. Then the dungeon precedes to teach you how to use that item. In Majora's Mask, the dungeons are built are around the use of your three main masks along with default Link, and they all force you to MASTER the mask before you even step inside the dungeon. So by the time you get inside the dungeon, the game goes to eleven. Why? Because you've already mastered the basics, time to go for the real game.
And this is why Majora's Mask is the best Zelda. It doesn't coddle, it embraces adventure, and it doesn't treat the player like a dirt person. Best Zelda.