read this a few years ago. Plot goes something like this, if i remember correctly:

1. boy raised as a girl, and living as one
   2 boy walks home with a classmate(possibly childhood friend) which he's had a crush on
   3 Boy confesses to girl about loving her, and ends up having sex with her
   4 girl finds out about the boy's real gender and apparently his "sister" is also the same.

i think this was how it was, and i think i read it on lu.scio.us, however i couldn't find it on the new site nor g.e-hentai.org.

You wont find that independently because it's part of a book. I know this, but can't remember which book contains this, or the name of the chapter.