Do the R&R yourself or farm it out you must have valid info it was not messed up by you or them or you will be holding the TP rollOne thing I know about taking your vehicle to shop, pulling the AT and sending it out for a rebuilt, then installing it, cost most than a couple of bucks.
Only advice that can be given, if the shop doesn't repair your dislikes file a complaint with the better business bureau or hire an attorney, or go to a small claim court, really not small claims, most up to $10,000.00. Had to do this when my kids away from home had bad work done.
Now if you are doing this work yourself, may be able to answer some of your questions.
Ha, could post the name of the shop and address so we know not to go there, but first step is to learn what the shop will do.