Did you make much use of the Inverted Song of Time? I was in the same situation as you the first time I really played MM, I putzed around in the game as a young kid and then actually tried to beat it as an adult. I’m no pro gamer by a long shot but the inverted song of time basically made the time mechanic a non-issue for me.
When you’re thinking about what to do next, try to divide the game into major milestones (pre-temple stuff, temples themselves, etc) and then follow the loop of (1) slow time (2) do major milestone (3) go back to town, deposit money, start over. It’s a little tedious, I know, but tbh I think taking small breaks to collect yourself between major milestones is a good way to approach adventure games anyways.
And, as the others said, you’re shooting yourself in the foot if you ignore the side quests completely. If you do all of them, the final boss will be one of the most fun, one-sided beatdowns in video game history :D