Well my favourite MCR stories are 'My Chemical Romance' (by XCyanide_SuicideX) (although its not based in high school, its still amazing) 'My Sweet Ride To Hell (mostly Gerard) and the sequel Not Even For The World (mostly Frankie) both by InkiNmyVeinz 'Milestone' it begins in high school but they graduate a bit into it (by chlc) 'These Bright Lights Have Always Blinded Me' amazing. mostly Gerard. (by deathXbeforeXdisco)
"Typical Girls" and "Forever, Now," both of which are linked on my profile. The first is a high school fic that has some slash but doesn't feature it predominately (it's mostly Gerard / Lyn-Z), and the second is a kidfic that starts leaning heavily toward implied Frank / Gerard near the end. I also have a MCR fic called "No Man's Land," but it features the characters as adults (around the time of the world tour for The Black Parade). I warn that it starts out painfully amateur, as well, but that's understandable since I started it more than three years ago...