Manga

So...I just did an advanced search on mangadex including the tags Genderswap, Girls Love, Harem, and Isekai and I ended up with just a single result: Harem Yori Heion o!: Isekai de Shizuka ni Neet Hime Sasete Kure.

I read the first couple chapters for you and...I think I found one of my favorite translator's notes ever:

So, if you don't mind getting pretty close to the hentai side of the spectrum, it could be the one for you!

Back in non-hentai world, I actually like this series with a title too long to include here. Yeah...it has slavery...but that has kind of become part and parcel with isekai at this point. It never really comes up again after the inciting events in the beginning.

The last series I have is another that I have read what was translated so far and really liked it: Did I Seriously Just Get Reincarnated as My Gag Character?!. In fact, it wasn't until writing this just now that I realize why the scanlations stopped, it has been officially licensed. So, pardon me while I get that real quick... Anyway, I love a good chuunibyou, and Nacht from this series is a great one. I binged the hell out of this series when I first found it and cannot wait for more.

Two come to mind but I don’t think their “wow I’m a girl and that’s what I wanted!” as much as they become comfortable and accept themselves.

“Life with an Ordinary Guy Who Reincarnated into a Total Fantasy Knockout” and one of the OGs, “Ranma 1/2”…

though the latter may not completely count, in the later seasons Ranma becomes much more comfortable in his female form.

I don't read much manga, so perhaps this is a common title but "Inside Mari" resonated with me on a substantial level. I only know of it from being posted about it in a few trans spaces. If you haven't read it, I'd recommend to going in blind. It seems like a cliche freaky friday body swap but it's something much different.