I have a 99TA with about 120,000 miles on it and I have had a SY3500 for about 2 years now. For the past month after I drive around let's say about 20 miles I hear a little hum noise and when the tranny shifts from 1st to 2nd.
Bang!! its like a punch in the back. From 2nd to 3rd is just a little smoother but still obvious. Does this mean rebuild or is there some particular part that goes bad after a while? Anyone see this before?

 

What are your tranny temps? Sounds like you're ok until the tranny gets hot. Maybe a cooler line is blocked and its getting hot and going into abuse mode.

 

This is from my site's Chronology page:

The car has been shifting hard and an engagement from Park to Reverse or Neutral to Drive would cause the car to jolt. The car is brought into the dealership where it is road tested and hooked up to a computer. A stored code, P0748, is found indicating that there is something wrong with the pressure control solenoid. The solenoid is eventually replaced under warranty and I was able to drive the car again at 4,896 miles. So far, so good.

I have a 2002 Z28 and it's completely bone-stock.