You need to keep a couple of things in mind too - such as your tune was scaled the "old way" - used airflow tables instead of the double stoic method... Unless you've completely retuned it - your going to want to almost double the values to begin with... I always try to shoot for over what the transmission will ever see - especially if it's a near stock trans - this will really help with shifts... I've seen "dialed into actual" torque models keep tranny's from making the shift in time no matter how much editing was done to the trans side... Try to target 900 to 1000 in the torque output at least...
These transmissions have to be run hard to learn in - don't be afraid to go at least 3/4 throttle when doing the initial shifting learn - this is even per GM after doing the initial relearn on the scanner...