Chrysler cirrus 2000 transmission?

i bought a car on craigslist and that day i drove it from VANCOUVER to portland and it work really fine...the following day i drove it to school and back home but i notice a little jerkin and after that day..i drove it on an hwy and it jerk big time...i took it to the auto shop and they said it is a transmission problem that the transmission in it has been flashed and that means it wont take there computer and that i might need to change the transmission for my CAR and they said its cost like $3000...pls i drive a 2000 model chrysler cirrus,is the transmission that expensive?