That was a nice post. I hope you will make more of them in the future and muse less about how bad you are, how easy the things you do are, or how bad something else is, whether it was a game or a replay. Those are the things which drive people away from you, like in that announcement thread for that recent game.
There were a few questions or insecurities, which I'll try to fill in. First of all, difficulty-wise I find IN Normal the most difficult Normal I've played. The scoring is very technical and multiple patterns are really difficult and mastering every single attack from the game will take a good while no matter how fast you were with it, IN has a lot of boss attacks.
For difficulties amongst the solo humans, it's generally a two-sided blade. Youmu has more complicated optimization and milking due to how the shot and her familiar act, in addition to also having to do most grazes. (the other humans often do at least some of the grazes, but unfocused and only for a time enough to speedkill the attack off, and I would rather sit in Mokou's fifth spell for twenty seconds unfocused than sixty seconds focused) If you wanted to avoid some of the grazing and picked a solo human other than Youmu, you would end up having a lot of other troubles, though. First of all, the difficult attacks will last really long and you will lose a lot of points if you focus through them, while Youmu can gain some consolation time from grazing focused. Also, certain stage portions will become very difficult due to either large damage radius, low damage or both. Stage 4 can tear up Sakuya and Reimu, and while they have some difficulty with stage 6B (Both have to go very high under the fairies, Sakuya takes long, and Reimu's slow movement makes it difficult to move around in time), it ends up being a hell with Marisa and her explosive shot, when the nut-case top-screen strategy from Easy isn't feasible anymore. (If I recall correctly, the current WR only breaks one familiar, which is a small wonder) In the end, I would rank Youmu a bit more difficult than the other shot-types, but it's really about picking your poison, to be honest.
In term of "mystery points", you're probably overlooking some cancels or nonspell milking efficiency. The fact that you get slightly more time from canceling bullets right as they spawn will play a role here with some of the fairies located in the later stage. If you wanted to learn the bonus cancel for the aimed fairies in the early stage, you could borrow a streaming below them-strategy, or attempt the one where you shoot until the first familiar has spawned, spin around to misdirect the familiars and then fire at the fairy with your familiar just as the fourth one comes out. Figure out a mantra or calculation in your head that you run through every time you face a fairy, and learn at which points of it to fire. This is in the case you want to optimize this portion, I wouldn't suggest it quite yet. I haven't seen your replay so I don't know of the other tricks you're missing. Don't you graze her first and fourth spell on Youmu? I thought it was worth doing. (They're worth around 400 and 700 graze, respectively)
The stage 3 nonspells are not that awful, especially in the case you're not attempting to graze them. This is mostly due to the fact that they're entirely static, based on Keine's position on the screen. I never found sight-reading them on Normal very difficult, but we come from very different backgrounds. To prevent strict situations on the boss nonspells, move around the clusters. I have noticed this is often feasible by altering between slightly left and right of the boss, where you should be located in the first place in order to efficiently milk the familiars.
For cues in stage 4, use the blue balls spawned by those large fairies. There is space just above where the lowest ones spawn in which you're supposed to fit into, and it will also act as your cue for what kind of a distance to keep from the fairy when doing the upward spin. The red bullets are aimed at you, and moving within a safe zone evades them completely, much like in stage 5, just less apparent to the eye and more difficult to execute.
I doubt doing the graze on Reisen's first spell is worth it unless you're going to graze the rest of the spell as well, it's only some fifty graze, and you most likely would get more points from shooting the boss. st would do it if it was worth, I believe, as it was a known strategy back when he did his run and he really used every trick in the book when doing that run. In addition to a couple of new strategies, which are together with the stage optimization what made the record as large as it is, not some idle grazing.
I personally found myself to be less consistent at Kaguya on Normal than I am at Lunatic, and sight-reading her first spell remains a mystery. I think there were some misdirection strategies devised for it years ago, which lost from twenty to ten million points in execution. Still less than failing the attack, though, and not that much altogether, considering the total amount of score moves in the four billion range. Salad is.. a fairly odd nonspell. You can figure a misdirection path for it (as the clusters move in the same general direction every time, altering a bit on Kaguya's position) and be rather successful in practice where your brain isn't a puddle compared to the moment you face that misfortune of an attack in a real run, where the bets are higher. For optimal play, you would want to time it down and fire at the familiars for as much as possible to gain extra time (I'd exclude the latter part until I went for 4.3B+ scores, and the former before I went for 4.2B+). You could practice the nonspell a lot in stage practice and become fairly prominent at it, but seeing people with thousands of Stage 6B credits fail the Lunatic version of the attack on their WR runs, I wouldn't count on that. Maybe safety bombing one non isn't that bad, at least for now. In my opinion, the Normal version of her second last spell is the most difficult one, as the Lunatic alteration has more spacey gaps. I wouldn't unfocus on the final spell. Not until the targets were high and WR-esque.
Good luck.