What I can remember is that it was over on fanfic.net and it was multi-chaptered with each chapter dealing with the Warbler’s understanding what Kurt went though at WMHS (and helping him to cope). I think in one chapter Kurt automatically went into the girls bathroom because it was second nature to him not to be allowed in the boys, and similarly in another he managed to get (blood?) stains out of one of the boy’s shirts because he’d been used to having to do it himself. Does this ring any bells?
Edit: I think that the chapter titles were one word on the content of the chapter, (there might have been one called "slushie") and in one chapter I think Jeff(?) liked to randomly pick up Dalton students just because he could and Kurt froze when he was picked up unexpectedly.
(I've tagged for bullying, because it covers the aftermath of bullying, hope this is alright.)
Found: Those Innocuous Moments by Mellony