Sounds like a shop owes you an explanation...and a transmission! You might also want to speak to a lawyer. You might be going to battle. How long has it been? Did they give you any written warranty? Do they advertise a warranty?
If you play your cards right you can get a Level 10 trans as a replacement!
'98 SVT Contour, in at least 639 pieces

4 Speed MTX...synchro and shift fork replacement in progress