GM495HP Crate Engine Idle Tuning and T42 4L70E Trans tuning

[Schwanke Engines]

Hey guys have a 53 Chevy Pickup we built that a customer insisted on running the GM 480/495HP Crate LS3 in with the 4L70E Trans. I dynoed the Truck and everything seemed good, but I cannot get this thing to Idle and work out nice at part throttle tip in and drive especially with the A/C on it will almost always die after a light throttle tip in then release.
PCM is an E38 from an 08 Chevy Pickup that is matched to the T42 module. Here are the issues Im having on the Engine Side of Things

1- The Idle issues where it wants to die when you give it a light throttle tip in then step on the brakes the Idle Drops when I do this around 2-300 RPM's it can catch itself without A/C on, but when It's on it almost always Dies.
2- I cannot get the PE tables to cooperate it was Rich on the dyno and I cannot get this thing to do what I want it to do as far as AFR's Go.

I am also having issues with the Trans shifting decently and working properly. Trans Issues are as follows.

1-first off it bangs into gear Hard when you go from Park to Drive.
2- It has a weird cut loose where it does not shift 2-3 shift then bangs off limiter
3- When I just drove it it wanted to almost go into a Limp mode when I hammered it in 2nd gear.

This seems like a lot, but I have never run this much engine with a 4L60E based Trans and E38 PCM. Any help would be greatly appreciated here, This has been kicking my ass for over a week. If it's easier/ better to go MAFless I will gladly do that, but have never done it on an E38 and am not sure how to set that up.