My barbaric girlfriend? He swap bodies with the girl he likes. It's mtf so maybe it's not exactly fits, but the female lead's everyday life (which in his body) is shown. There is romance

between 'her' and her bestfriend, but her bestfriend doesn't know her true identity

Quote from pipipierrot

I.S. might work? Though it's more like she has female body but male hormones due to being born with both male and female parts, but having to remove her male part as a baby since she would have died. The main story doesn't start until a few chapters in. Although this probably doesn't really qualify for transgendered, they face some of the same issues as trans folk, I suppose. It's really great, though! Incredibly realistic for the most part. I think you'd like it. http://www.mangaupdates.com/series.html?id=3344

Actually, I love that manga and it's one of my all time favourites 🙂

Boku to Kanojo no XXX has been marked for reading, will try and get to it in the near future.

To be honest, I was just getting tired of all the male to female gender-bending that has become the trope standard. MtF+Female and MtF+Male is apparently acceptable, yet FtM only ever goes so far as futanari like situations (and even then most of the times it's 'girl on girl').

I never did expect a 'serious' manga that tried to take a realistic look at such a situation (until I.S. that is), a manga that doesn't focus on fanservice or harem/ecchi is already a huge step in the right direction.
I suggested Shounen-Ai mainly because I believe that when someone changes sex it doesn't necessarily mean he/she changes gender and/or sexual preference as well. (I have a huge dislike for gender roles -> uke/seme, butch/femme, etc.)

If the tg loved someone before the change, he/she should still love that person after it.
If a tg falls in love after the change I would be interested in the psychological aspect... IS - Otoko demo Onna demo Nai Sei being a good example on this, albeit more about the social aspects and less psychological.

Kampfer might be what you're looking for -

Description
Senou Natsuru is a normal high school boy. One day he wakes up to find himself turned into a girl. A stuffed tiger "Harakiri Tora" comes to life and tells him to fight as a female psychic fighter "Kämpfer". Having no idea about what's going on, Natsuru is involved in the battles against other "Kämpfer".

The description barely sums up the first chapter though, I thought it'd be like generic Gender Benders of Cross-Dressing people and the like, but it's actually a very interesting read.

There are some elements of Shojo-ai, and it's a rather ironic Harem, accompanied by fast paced actions and plot twists, suddenly (though not disappointingly) having appropriate slow downs, only to rev up again.

Ame Nochi Hare (BIKKE)

Click.

Now that you say it, I notice most of gender bender genre are mtf... and comedic...

Have you read Claudine? Since she doesn't really change to male (there's no surgery that time), maybe not exactly fits. But I think it explore the psychological aspect of being transgender well.