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At first, when Peter Parker met Jessica Drew, his female clone, her existence alone was enough for him to be weirded-out. Okay, that was the second time he met her, the first he was far to panicked over Mary-Jane's disappearance. He was irrational, hysteric even.
The next time, Jessica seemed perfectly comfortable with her gender, and he didn't even pose to wonder how that was possible. (And neither did she, either.)
It's only after his pal Johnny Storm, the Human Torch, manifested an interest in dating Spider-woman that things changed. Sure, right back then he was convinced it was only weirdness of one of his best-friends wanting to date his clone that made him react so strongly. But when he got time to cool of a bit…
At first, he started to think that he may be gay, that maybe he wanted Johnny to look at him this way, to be his boyfriend! But then, without knowing why, Peter started to think of Jessica.
Somehow, Spider-woman seemed perfectly at home in her female body. In fact, even when he first truly spoke with her, she was raging about not having a past beside memories of his own far much that she was about being a girl. And even her few words about her womanhood sounded more like ‘Because of you, I know nothing about being a girl!’ than ‘If only I was (still) a boy…’
Finally, Peter realized he did want Johnny to look at him like he looked at girls, but not for the reasons he through. The truth of the matter? The Torch is a known womanizer, and him looking at you like that could only mean a thing: He's seeing you as a girl, and thus wants you in his bed.
Like a sudden illumination, this self-discovery made Peter understand something else about her, namely that what made things so hard with the three girlfriends she ever had so far. While she loved all of them dearly, (even if she wasn't sure which one she truly loved as more than a friend or a sister) said love was tainted by her jealousy of their body, of the fact they were as female on the outside than she was on the inside, unlike herself.
Of course, all this thinking took far more time than you needed to read up to that point, and the young miss Parker needed even more time to decide who she should discuss this with, how to say it… And, even, if she really should speak of it, or just try to ignore the problem altogether.
In the end she chooses to contact Spider-woman, thinking “If someone can understand me, it's probably Jess.” She was probably right, with how often Jessica must have wondered if she truly was a woman, albeit one with borrowed childhood memory in which she's a boy; or a man trapped in a feminine body, trying to convince herself she truly turned native.
After hearing all of Spider-man mental struggles, Jessica hugged her new found sister against her, trying to comfort her. (Must not have been easy, especially while trying to think what it could mean about her own identity issues.) The two stayed like this a long time, the transgender one crying on her clone's shoulder.
When finally, the girl still known a Peter stopped crying, her sister asked this disturbing question: “How should we call you now, sis?”
But said sister didn't think that far. “Wha… What do you mean? Why did you… Did you call me sis?!?”
“Because that's how I see us, as siblings. And since we established you're as much of a girl than me, your body notwithstanding, we can't call yourself Peter anymore, can we?” Then, seeing the look of horror and worry on her sister's face despite the mask, Spider-woman added. “Take all the time you need to choose your new name, one that will make you proud to hear when someone is calling you. It's important, the first step toward rebuilding yourself…”
To miss Parker, her sister sounded like she had some regrets over her own choice in name…