Jay,
I experienced the exact same scenario you're describing. I made a couple of posts about this situation in your "Diesel Dynamics pump kit first impressions" thread. There are several factors to the explanation of why your turbo is behaving this way.
1) The fact that you (and I) have a fully exposed air cleaner makes the noise from the turbo compressor much more audible.
2) Recent addiction to BOMBing the truck has given you an itchy right foot
3) More fueling, larger injectors, pump adjustments, drive the turbo to make more boost at a faster rate.
4)
Your new torque convertor This is the biggest factor. The reason being is that the much tighter convertor will effectively slow the engine down quite fast when you back off on the throttle. When you let off of the throttle, you remove the turbo's drive pressure..... this coupled with a rapidly slowing engine will make the turbo unable to maintain boost..... then you get surge ("bark").
The root of this surging is, however, the turbo itself. It's the design of the compressor wheel, the compressor housing and the clearances between the two that will determine how the turbo will behave. The only way you're going to eliminate the surge is if you change your turbo.
Cheers,
Sean