Make it clear to them that you can no longer recommend their service to anyone you know. The probability of your flexplate failing is already ~ 0, add in that they did remove the transmission, and this entirely indicates that they are really trying to rape you. Why would you pay the same shop to fix what they broke? Go to a different shop if you feel that they won't fix it for you and you have to pay anyways. Otherwise, they will just keep raping you. Next time, you'll notice that the TOD mounts have failed, and the transfercase needs to be replaced.....

Get real Breezy - no one in these sorts of business is honest.