dude you're drowning in a glass of water here. don't overcomplicate things. it really sounds to me like you are talking about the pcs software here, but if you're talking about tuning the tcm via hptuners then let me know and I can address some issues in regards to that.
which tune are you talking about dialing in? if in fact you are talking about the pcs software, that isn't how the transmission is tuned. anything with shifting/shift points/speed/pressure/etc, etc, etc, is done with hptuners. if you're messing with the settings in the pcs software, stop. only a couple minor things need to be adjusted in there (rpm pulses and tps min/max) and the rest should be left alone because it doesn't need to be altered, doesn't tune the tcm, and will just create problems where there would otherwise be none.