The first clue that Sasuke's peers had that something else had been flipped in SasukeLand aside from the near 180 degree turn his cheerful personality had taken had been the hairclip. Had Sasuke's mother's clothing not been packed away into storage along with most of the belongings of everyone else in the clan, chances were that Sasuke would have shown up to his first day at the Academy since the Massacre with more than the hairclip to mark his ambitions to womanhood.
Nobody really payed all that much attention to the hairclip despite the fact that it was rather sparkly and had what looked like real diamonds set in it however, as other students had shown up wearing far stranger before, up to and including the time Naruto had shown up wearing a sparkly pink leotard and an orange cape. Everyone noticed when Sasuke attempted to join the girls when they split off for their Kunoichi classes however, and the class' new Instructor - a young man who was still in his teens named Umino Iruka - quickly grabbed the boy before he could join in on the flower arranging lesson. Despite the fact that he got clawed and bit for his efforts, Iruka dragged Sasuke kicking and screaming over to where the boys were being given a lesson in carpentry, in case they had to pass themselves off as laborers during a mission.
Most people would think that many of the lessons the girls were taught during their special Kunoichi classes, such as flower arranging and the like, would be useless for life as a Kunoichi, and that they were there merely for tradition's sake since they had been part of the curriculum since the Nidaime had founded the Academy. This wasn't entirely so however, as Kunoichi were expected to be able to pass themselves off as civilian women from any social strata at a moment's notice, and part of that was learning a traditional art that, while becoming considered to be exceedingly old fashioned and out of date amongst the general populace as a whole in these modern times, was still something of a hobby for the upper middle class or the rich.
Sasuke, who had not yet realized the difficulty and the likely impossibility of the path he had chosen to take, had decided that taking the Kunoichi classes would be his first step in becoming the girl his parents had wanted him to be since the Kunoichi clases were reserved for girls alone. Of course, getting around his homeroom teacher in order to attend said classes was another matter entirely...
The second clue those at the Academy had been given that something else was off in SasukeLand aside from trauma from the Massacre had been when he'd started signing his homework with a different name upon his return to said Academy. There had been some small bit of confusion for Iruka over who this Kushina person was until one of the Instructors who had worked with Sasuke's class before Iruka had started teaching recognized Sasuke's handwriting and clued him in. Any subsequent attempts he made at getting the boy to sign anything with the name he'd been given at birth were made in vain. Rather than getting Sasuke to sign his name on his work properly, he had instead convinced the boy that there was a need to go to the registrar and have his name changed on the class' roster.
Every time Iruka saw the name Uchiha Kushina below that of Uzumaki Naruto - which had him frowning as something about the name in relation to Naruto's was niggling at the back of his mind - he would let out a frustrated sigh and make his way to the Academy Registrar's office in order to have it corrected. He was sure that Sasuke would eventually give up and that whatever the hell sort of phase he was going through would pass before he graduated the Academy. It didn't really bear thinking if it didn't, because anyone who worked with Sasuke after he became a ninja would give him funny looks over his choices at the very least, and would more than likely pick on him, which would likely end up triggering a violent episode.
The Third and most major clue that there was something other than trauma from the Massacre going on with Sasuke, which had even the most unobservant villagers sitting up and taking notice, had been when the boy had finally used his allowance from the trust fund which had been set up for him when he'd inherited the pooled assets of the entire Uchiha clan to purchase a new wardrobe. The boy still dressed like a typical Uchiha, but the gender of the Uchiha he dressed like now as compared to before had been reversed. Rather than sticking to his navy blue top with Uchiha crest on the back and navy blue shorts combo, the boy had started wearing skirts and dresses in the rather conservative shades that were favored by the women of the clan, most often wearing a navy blue skirt and low-collared navy blue top with a mesh shirt underneath.
This last had helped Sasuke unknowingly dodge a bullet, and gave Neji yet another reason to curse his fate. The budding fanbase that had been forming amongst a group of his female classmates who were just beginning to depart the "boys are icky" stage rapidly vanished after Sasuke had started dressing like a cousin of his whom he'd admired when they collectively decided that he was weird rather than cool and tragic. Since Sasuke was out of the picture, they turned their focus on the cool and handsome boy in the year ahead of them who had the bonus of being older, more than doubling Neji's completely unwanted fanbase.
Iruka, who was rather new to the whole teaching gig, was at a loss as to what to do about his student, seeing as the therapist he'd spoken to about Sasuke had marked the boy's behavior down as "I've got ninja who've watched their teammates be tortured to death before they themselves have been tortured to near insanity. I've got ninja who've been brainwashed into turning against their own village, and a ninja who'd been given a post-hypnotic suggestion that had caused him to kill and eat his own children, and you come to me with this?!". Try as he might with as few resources as he had however, there was nothing he could do to correct his student's behaviour, as the child continued to insist that he was a girl named Kushina.
The new name was the least of his worries when dealing with the boy, since there weren't any laws against using an alias for non-criminal activity, so, there was really no point in getting into a struggle with the boy over a non-issue, since Sasuke could technically use the name Kushina whenever he wanted to as long as he wasn't committing a crime while using it. That, and the Academy registrar was getting sick of the sight of both of them.
After the second time he'd tried, he'd learned from the Academy Superintendent himself that he couldn't ask Sasuke to go home and change, since what he was wearing technically didn't go against the Academy's dress code which was remarkably permissive. Thanks to the wildly varying dress that had been adopted by the various ninja clans over the years, the Academy dress code had basically been boiled down to "As long as it covers the genitals". Boys dressing in women's clothing and vice versa wasn't even covered.
In the end, after he'd been thwarted at every turn by the boy and his supporters who likely found Sasuke's behavior amusing at the very least, he decided to adopt a wait-and-see policy in regards to Sasuke, hoping that it was some sort of phase that the boy would grow out of, rather than a sign of something major lurking beneath the surface. He didn't want to potentially ruin the child's future career by conflating the issue with the whole Massacre thing and calling the psych team in for something that could turn out to be relatively harmless and stem from something other than trauma from the Massacre. It wasn't as if he hadn't seen "Kunoichi" with five o'clock shadows before. They generally weren't well accepted within the ranks however, and he didn't want to see that happen to Sasuke. But, fighting the boy over it had caused him to become even more stubborn and resentful, which was completely opposite to the effect he wanted.
In the village outside the Academy, there had initially been a great deal of gossip about Sasuke and the possible reasons for his gender confusion, as it had all the elements of an interesting story, but the whispers had eventually died down when someone pointed out that he was nothing new, as the Uchiha had had a similar family scandal at least once a generation, with the latest being a second cousin twice removed of "Kushina's". The civilian boys in the village and even some of the younger Genin rather quickly learned that picking on Sasuke was a bad idea, and generally didn't try it a second time. While Sasuke wasn't on Itachi's level, he was quite talented, and had several years of clan training under his belt. Other than a few off-color comments, the men in the village generally left Sasuke alone, because they didn't want the trouble they'd get in if they messed with the "Last Uchiha".
Amongst the Ninja ranks, word of Sasuke's life choices made its rounds and, as it was irrelevant to their lives and increasingly became old news, it was forgotten in favor of things that were more relevant to them by all but those who dealt with Sasuke on a daily basis. Forgetting things that would be practically earth-shattering to others but irrelevant to oneself or one's current mission, was a trait that was common amongst ninja, and seemed to be handed down to their children, with an extreme example of this being one Uzumaki Naruto who had forgotten things during his life that would have had the Intelligence department salivating had they known the information existed.
As for Sasuke's - who shall henceforth be known as Kushina - Academy class, well, as the years passed, the students all but forgot that there had once been a boy named Sasuke in their class despite Iruka's constant efforts to remind them in hopes that it would cause Sasuke to stop what he was doing if everyone treated him like the boy he was. It was completely understandable that most of the students didn't mentally associate Kushina with Sasuke though, considering the fact that Kushina seemed to be a completely different person from the cheerful and helpful little boy who had picked up the moniker of brown noser which had never been used to his face because of who his clan was, and who he was within that clan. As for Kushina, as far as the students in Umino Iruka's class were concerned, she was that weird girl who sat by herself, scowling at everybody when she wasn't giving Naruto strange looks or showing off during weapons or Taijutsu practice. Just about everybody was envious of her talent, but, aside from Naruto who challenged just about everybody, they were too afraid to approach her in order to challenge her in case she snapped.
As for why Kushina gave Naruto those "strange looks" that her classmates noticed and commented on, there was a bit of a story behind that, and - contrary to what the class seemed to think - it wasn't because she had a crush on him. The source of those strange looks had been a photo album. It was possible that the evidence of Naruto's parentage lay forgotten amongst the pages of dozens of photo albums across Konoha, and the Uchiha had happened to possess one of them. Had Kushina remained Sasuke, this album would likely have gone forgotten after Itachi's face had been scratched out of all of the pictures since it had been more of a "friend" album, and there had been another album that had contained photos that were exclusively of the family together that he would have spent more time looking at.
While Kushina had been going through all of her mother's photo albums, scratching out Itachi's face wherever she found it, she found a photograph which had been labeled with the name her mother would have given her herself had she been the proper sex at birth. In the picture was a pair of Academy students, a slightly girly looking blond boy with blue eyes who was looking at the camera and smiling, and a girl who looked like a red-haired version of Naruto who was glaring daggers at the boy in a manner that was entirely Naruto. It was quite obvious to her that the two were Naruto's parents. A further search of the album revealed that that wasn't the only picture that her mother had of one or both of Naruto's parents. In all of the ones of Naruto's mother, the girl and later woman was doing something that was very Narutoesque. Every time Naruto did something stupid, something that resembled what his mother was doing in her mother's pictures of her, Kushina would look at him and wonder exactly how and why their mothers had been friends.
And so, things continued for nearly four years. Towards the end of her days at the Academy, Iruka eventually gave up on changing Kushina's mind about being a girl, since every method he attempted including giving her the straight facts on what tended to happen to transgenders amongst the ninja ranks - especially when they got into enemy hands - had failed. The villagers moved on to better and juicier topics of gossip, treating Kushina according to their views on transgenderism which was either positive or negative or everything in-between. The Ninja didn't pay too much attention to Kushina other than to do the standard threat assessment as they passed her on their way to other business, unless they had business with the child who was shifting from the "male" category to the "female" category in their minds as they marked her in their mental files. At the Academy, things were both the same as they would have been had Kushina remained Sasuke, but different as well. Kushina was as cold as ever, at the top of her class, and had Naruto constantly trying to outdo her, but then again if you put Hinata at the top of the class, Naruto would have tried to outdo her too. However, rather than just being unpopular with the boys who had disliked the post-massacre Sasuke for his attitude and the fact that he was constantly showing off, Kushina wasn't all too popular with the girls either, because they thought she was a creepy stuck-up bitch.