Harmonic Feedback by Tara Kelly is an excellent book. The MC has a case of Asperger's.

I was going to mention Harmonic Feedback as well, definitely an awesome book!

(I wholeheartedly second Harmonic Feedback. She has Asperger's & ADHD)

Five Flavors of Dumb by Antony John is AMAZING and, from what I remember, pretty clean. The MC is deaf AND it's a book about music. Dude. It ROCKS. :)

I don't know if it's considered YA (it might be more MG), but Out of My Mind by Sharon Draper is supposed to be excellent (my kids have read it, but I have not had the chance yet). I also recently read Shark Girl by Kelly Bingham which is a novel in verse about a girl who loses her arm in a shark attack.

What about Percy Jackson? ADHD, dyslexia?

Good luck. I went over every book I read for the last 5 years. Not much there. Unless having super powers count as a disability . . . Then I suggest Hidden Talents.

The Lovely Shoes by Susan Shreve about a girl who's born with a birth defect. It's middle reader, so probably won't work for this, but it's clean...

There's also Mockingbird by Kathryn Erskine. It's ages 10 and up. National Book Award winner about a girl with Asperger's.

Stuck in Neutral by Terry Trueman was really interesting, about a kid with no muscle control at all and what it might be like to have no way of communicating. It had a little teen boy humor, but was quite clean.

Haven't read it ourselves but we hear Marcelo and the Real World is pretty good. Not sure if it's "clean" though...

The sister of the protagonist in Chime (great book) has a disability too.

Hunger or Rage by Jackie Morse Kessler. Hunger is about a girl with anorexia and bulimia. And Rage is about a girl who cuts herself.
Don't know if this books are what you are looking for but it's the only ones I could think of. Hope this helps.

My recommendations are Five Flavors of Dumb or The Running Dream. Both are very good!

It's more MG but Rules by Cynthia Lord has several disabilities. Awesome book.

I just sent you about a bazillion DMs, since I can tweet right now... :P

In Noah Zarc by D. Robert Pease the main character is paraplegic, but it's futuristic so I think he uses a special body suit to get around. Not sure if that counts for your assignment. I haven't read it so I don't know if it's any good. Good luck on your search! Sorry I can't be of more help.

the running dream is good also m not sure if its a YA book but House Rules

Wonderstruck by Brian Selznick is AWESOME! And it has two disabled protagonists, one born deaf, one with hearing loss.

Saffy's Angel by Hilary McKay has my favorite wheelchair-bound girl, EVER. She's not the main character and her disability is only a minor theme.

Rules by Cynthia Lord is pretty good -- I listened to it on audiobook.

Personally I didn't love Out of My Mind and couldn't get very far at all in Mockingbird (too close to home).

There's also the famous The Curious Incident of the Dog in the Night-time by what's his bucket. Mitch Albom.

Awesome mystery book with autistic protag: The London Eye Mystery.

Also Al Capone Does My Shirts by Gennifer Choldenko has a major theme of a sibling with a disability.

Freckles by Gene Stratton Porter was a bestseller in the early 1900's and the MC has a physical disability. Personally I like a couple of her other books better.

Now I can't speak for Curious Incident having not read that one, but all the others are squeaky squeaky clean! Let us know what you pick!

Probably MG, but, Firegirl by Tony Abbott.

I see Tara already said it, but Harmonic Feedback is amazing, although Marcelo in the Real World by Stork is cleaner. I PBRed that one.

Joey Pigza Swallowed the Key by Jack Gantos

Cryer's Cross is a great book about a girl with OCD. It's somewhat of a YA thriller (IMO).

I want to heavily second The Curious Incident of the Dog in the Night-time. It's amazing.

I haven't read it, but isn't Sign Language about a hearing impared person ? I'm not sure

Farsighted by Emily Chand is about a boy that is blind. Its a pretty cool book. No sex scenes and Im pretty sure no cursing. not 100% positive though

Harmonic Feedback is a great one.

I also think of North of Beautiful - while not exactly a disability, it is a disfigurement in the main character that greatly effects how she lives her life.

Among Others by Jo Walton - the MC is crippled in one leg and uses a cane which causes her to be viewed as an outsider.

Although I personally don't really consider deafness a "disability", I would recommend Five Flavors of Dumb by Antony John and Read My Lips by Teri Brown. Both are really good.

The educational system (at least according to my textbook) considers it a disability. However, being gifted or talented is also considered a disability. So... take it for what it's worth.

Gathering Blue by Lois Lowry or The Only Alien on the Planet by Kristen Randle.

The Running Dream is YA and definitely fits the bill!