EDIT: I almost forgot one important part. I learned that if you pick Luigi as your character, you get more time loss than Mario. There's about a second to two seconds difference of start up and I am not sure how long cutscenes are with his extended noises. So basically choose Mario, not Luigi.
So after never playing this game for years and touching it again just to run it, I learned a few important things that I haven't seen in all other scores. Since the story mode in general is the same length across all difficulties (Normal and EX are split up though, still.) all saves will apply across each difficulty.
B to D : I learned this one fooling around with my brother. Before I was always aiming for "A" because obviously it's the best score, but I learned that by getting below an "A" but above an "F" (with exception of Bowser's Castle.) you chop off about a half second, which matters once all the chopped time is put together after each song. This occurs because the game has a longer want of praising at the grade screen. I do not know why it does this, but it is there. The only risk is the dual songs, since you are still aiming to win. In this case, best shoot for a B by just missing a few notes, not too many.
No Memory Card : Another time saver, about two to five seconds depending on how long the loading takes. Very simple: load your game and remove the memory card. Before starting a run though, play a song and finish it (fail or clear, doesn't matter) and then you will be prompted to insert a memory card or continue without saving by choosing yes. Choose yes and you're done. Free time save.
World Mini-games : There is only two mini-games where you must fail to save time, and those are "Run" and "Avalanche." Both of these are easy: for run, just don't do as prompted, it saves seven seconds. Avalanche you must interact with. Move in front of a snowball and get hit, since it will save you over twenty-three seconds.
RNGames : This is the main determiner of runs in this game. There are four bonus games in the regular Story Mode, and those are "Coin Collecting," "Wheeee!," "Hidden Treasure," and "Brick Breaker." Out of all bonuses, the shortest is "Brick Breaker" (10 seconds on Go) and the longest is "Coin Collecting" (30 seconds on Go). The other two are tied up almost, but "Wheeee!" has a slight lead. I would recommend that if you get "Coin Collecting," end your run immediately and restart. There is no saving yourself with that mini-game. The perfect RNG run would be all the bonus games being "Brick Breaker," and combined with a flawless over world navigation and menu/dialog mash, there will never be a faster time.
These are very simple things to remember, and it will improve the time a lot. Since I started I've gone off the fastest times in all difficulties, not just one difficulty, and doing this gives a three minute lead against everyone else around 59 to an hour.
