Wow, that is awful. Were you able to have a necropsy done? You should probably contact the breeder or pet shop you got him from. Could be an illness that other hatchlings in their collection/inventory may have, or maybe even your snake was from a clutch with a lot of deformities or babies that didn't make it. :/ It sounds like your husbandry is just fine, so I'm thinking it has something to do with the breeder (illness, bad clutch, whatever).
Just edited to add, that the weird neck position really makes me thing that maybe he came from a messed up clutch. Could have even been a difficult hatchling from the start. Maybe ask the breeder if he started off eating/shedding/pooping okay or if he had to be assisted in any way?