i sure would hope a built trans would be able to handle a simple tuner. try different tunes maybe but the bottom line is that this type of story is not unheard of when it comes to ATS trannys.Take the tuner off and return it to stock, if your transmission survives, then it's your tuner.
I would bet your tuner is killing your transmission, FWIW...
go with a Twisted Diesel or Elite or RCD or one of the many trusted, proven trans builders.