There's not much that can be done to the transmission without taking it from the car, and dis-assembling it. There's no pan to remove, and the only filter is inside the transmission, where it can not be accessed with out taking the transmission apart. Also, there's not much to adjust. The fluid is probably not synthetic, and it does need to be changed occasionally.
If they "took a few things apart", they probably went inside the area containing the valve body, and removed "a few things". I've got a suspicion that your problems could be related to their "taking a few things apart". Don't know, just a guess.
