Turbo cough or (bark)
I have cut & pasted a post from the past which helps explain why this is happening.
My 98 does the same thing and is very loud at low speeds. I have twins and an open K&N air filter so the turbo whine is very audible and will (woof, woof, woof) if I release the throttle suddenly at low speeds, let me attempt to explain. When under power and creating boost the drive pressure in the exhaust drives (spins) the exhaust turbine which in turn spins the inlet compressor. As long as these conditions are stable the exhaust drive pressure maintains the energy to turn the turbine wheel creating boost. As soon as you release the throttle no fuel equals no energy from combustion heat which means no drive pressure. In an instant (under certain circumstances) the boost pressure can exceed the drive pressure, now the airflow (boost) which was being driven into the intake reverses because the energy driving the air pump (turbo) is essentially shut off. The air flow reverses and can back flow out through the air filter. I'm not a turbo expert but I would say a steady diet of this if excessive is not good for the turbo because the turbine wheels are being slowed down extremely fast which puts excessive loads on the turbine shaft bearings and seals.
The Phatt Shaft turbos are an attempt to eliminate breakage due to this phenomenon.
There is no performance advantage to the larger turbo shaft other than increased durability.
The most likely reason you are just noticing it after the mods is because the air box is modified, it was designed to quiet the inlet noise from the turbo, (noise pollution).
Your signature shows that you have an ATS 5 star TC as I do. This can also contribute in the following manner. When towing you can load the engine and build boost very at low engine speeds, and when the throttle is released your ATS TC slows the engine so fast that the boost air flow reverses.
Performance mods Chip, exhaust, intake and transmission along with towing combine to make it much more noticeable.
Turbo bark is most noticeable when towing or working the engine because significant boost is being generated. A modified air box will also contribute to more turbo noise because the air box was designed to quiet the inlet noise from the turbo, (noise pollution).
Hope this helps
Tim