A transmission swap on an MTX Contique is billed as a 10 hour job, at 99 bucks an hour (at least out here in cali) so there you go, a thousand bucks right there. I would assume an ATX is more time-consuming, but don't know for sure.
When I had my Galant, I had that same type of warranty that made an inspector come out. When the engine failed, the inspector approved a rebuilt one, but I wanted a new one so I paid the difference ($600 bucks) for a new one...you might have the same option. Be sure to ask!
Good luck,
Matt
