If you had the superchips tuner you should have loaded it back to stock before taking it to the dealer back in June. Why else would they give it to you?
Good luck on this one. I don't think you will get very far with GM and it is out of the SLP warranty.
I think the idea of the Superchips tuner in this case, was only to put the factory tune back, for dealer only purposes, so they'll be able to do pcm related work with GM approved devices. Probably SLP has a tuner lock option for their tunes, so nobody is able to see what they did, i hope this is not the case, and the calibration is wide open, in any case, more likely it was not for the owners to load the factory tune and drive to the dealer. Having the factory tune loaded with a supercharger is not good at all. and i'm sure SLP must have some sort of documentation that describes the procedure.
This case should proceed well with some patience, hopefully. The car came with the mods, and while is out of SLP Warranty, GM should cover the repairs under the 5year/100k miles waranty for engine/trans, it's not like the OP modded his car up like most of us would do, he bought a factory performance package in agreement between SLP and GM. i think the issue at hand, is that along the line, one monkey at the dealer/GM regional rep, didn't know how to document the vehicle as it should, it's the same thing as buying a Roush or Saleen (when it was in existence), Ford would warrant the vehicle, in this case GM should do the same thing.
OP, has GM contacted you to ask for the car documentation where it shows VIN number, SLP/GM agreements and what not ? you might have to engage SLP now, to see if they can also make some phone calls/send documentation etc, more likely this would be a misunderstanding where unfortunately, you are going to spend more time on it than what was needed originally.
Crap it would be interesting to know what SLP did with the trans tune, i wonder if that calibration can be read with HPtuners, If so, i could help pinpoint if there are any obvious issues in the tune, that would lead to a failed trans, although, i'd think if the modifications and tune had GM blessings so people could get the car the way it was, that the tune was certified by somebody in GM, like they'll do with their standard products.
At this point, all you can do is wait and try to move the connections between SLP and GM to speed up the case, if you don't want to wait, i'd think the cheapest alternative would be a used trans with low mileage from a junk yard, perhaps a new trans from the dealer, like MGMGT have suggested, or pay a little bit more and have the thing rebuilt, circle D rebuild is cheaper than Century transmission, if you get it rebuilt, you should consider asking the builder about the clutch packs, and how close to stock they're in thickness, thicker clutches would affect how the incoming/outgoing preset volume pressures are defined in the tune, if they're thicker, you'll have to modify those volumes values in the tune to account for them.
I believe Rick Crawford can help you understand this better, as he has done rebuild in this trans, there isn't a lot to change inside the trans to beef them up, and one of the reasons why most companies doesn't like to work on this trans, aside from the fact that some tuners like to splash their fingers in the tune, thinking the trans would shift like the one in a BMW M3 or Nissan GTR for example, aint happening, and the reason why they're getting premature clutch failures. This trans are tough, they're just misunderstood on how deep we can push them with regards of shift speed, pressure and TM wise, especially when the car is making some good power. think about it, people want the barking tires feel, they want neck snapping power out the trans, and that's with just a CAI, add a supercharger and how long are the clutches supposed to last when the tune is abused, or the tuner have no idea what he/she's doing other than zeroing out shift speed, quadrupling shift pressures and zeroing out TM. not saying this was the case with your TCM tune, but would you ever know ?