Ok - if you're supposed to have any recall work done, then have it done - and then get out of there. $6500 for a transmission? Was that a typo? Are they going to gold plate it? I think that's the "the sales department would love to show you our new...." price.
I am not familiar with this recall. But if the car is covered under it, have the work done. Then if the car isn't shifting well, take it to a reputable, local, independent transmission shop.