Welcome to the I got hosed club. It happens, and when you come on here it makes you feel like a dumbass for not knowing the easy signs.
luckily, parts are very easy to find and pretty cheap. i bought used cases, with no chain wack for 125 bucks shipped to my door. a complete stock trans is around 100 bucks.
the write up on here, and in the clymers manual you should be able to take care of it yourself. if you are unsure, send it to one of the sponsors, HJR, Wildcard, FAST. they are all great guys to deal with.
i reccomend while you have the cases split, to spend the extra 50 bucks and have the crank trued and welded.
and dont let the dealership work on your quad, they will rape you in costs, and it will run shitty when you get it back.