[1KillerSS]

If you have HPT, I can look at your tune for you, I'll tell you for sure whether or not its suspect. There is more than just one place to enter a number in, if you want to set/change a rev limit. Yes there is one obvious box to enter the number in, but you also need to change a few other values in a few other places.

cutoff rpm VS gear
lamp rpm
wheel speed limit
extreme cutoff
extreme resume
startup modifiers

The control methods need to be properly selected, whether or not you use fuel, spark, ETC, or a combination of them. I am also not blaming your tuner, but if he is not familiar with ls engines or GM tuning, or even the E38PCM, which itself is a PITA, then its easy for someone to miss something.
I would do your tranny just to be safe, that's just me.