After all I decided to replace all social links, since many of them affect the rest, and it's easier than replacing one by one.
I'm currently checking Junpei and Rio's links, and everything's going fine.
For reference, here's how I did it, and the files involved:
1) In Persona Editor, I replaced the npcCMMtable.bin of the male protagonist (inside init_2.bin) with the female equivalent (inside init_2F.bin). This places the NPCs in the map, and enables the dialogue to initiate the link. There are several files inside:
-NPCSwitchFlag.dat: I believe this activates the NPC on specific days (for example, Rio is available on Monday, Wednesday and Friday). Restoring the original .dat made her available on the same days as Katzushi.
-cmmScript.bf: The dialogue to start social link. Both the flowscript and dialogue can be edited with AtlusScriptCompiler. I restored the original dialogue and flowscript for Yukari, Mitsuru and Aegis. Specially Yukari, since her link begins much earlier in the female route, and I didn't want that.
-Several .dat files, numbered 01 to 26: Maybe they're the models and positions of the NPCs. For example, replacing m24.dat and d24.dat caused Nozomi to disappear from the fountain square. Maybe useful, if one wants to replace just one social link with a custom one.
2) To fix the Social Link screen, I changed several files inside cmm.bin (also inside init_2.bin). Most of them can be edited in hex:
-cmmName.dat: the name of the Social Link.
-cmmDiary.dat: the text on the calendar for every day.
-cmmHelp.bmd: the descriptions of people from S. Links.
cmmEventNo.dat tells the game which events to display: the ones from the male route, or the female equivalent. I left it untouched, since I only want to replace specific events, and not those of the main story, for example. The names for the Courage/Academics/Charm parameters are also in one of these files.
-The portraits seen in this screen are in data/commu/bustup.
3) Replaced some events with their female equivalent, also with Persona Editor. Only those of the S. Links that differ, the rest load the male version by default.
The Sunday phone invitations and dates don't have an alternate version, since both are contained in the same script. However, this can be edited with AtlusScriptCompiler or in hex. The function that checks whether the character is male or female in the script is:
( BIT_CHK( ( ( ( ( 0 + 0x0400 ) + 0x0800 ) + 0x0400 ) + 8 ) ) ) for male protagonist
( BIT_CHK( ( ( ( ( 0 + 0x0400 ) + 0x0800 ) + 0x0400 ) + 7 ) ) ) for female protagonist
I also deactivated Yuko and Maya's links, to avoid them being initiated by accident, and later conflicting with Koromaru and Saori.
There are still a few things I haven't fixed. For starters, there are occassions in which there's an invisible Koromaru and Ken in the dorm at night.
Also, I can't edit the name under the card in the S. Link screen (as seen below). I suspect it may be graphics and not text. But I can't find them. Replacing the cmmFormat.dat changes it along with the portrait, but messes up graphics when switching between links, and eventually freezes the game.