Did a search, but didnt see any responses that were on point. Situation is as follows:
02 TransAm convertible, approx 90k miles, original 4l60e tranny
new poly engine and transmission mounts
did an engine swap from the LS1 to an LQ4
less than 3000 miles since the engine swap
no new cam, torque converter, etc.
799 heads
ls6 intake
PCM tuned for the new engine and had them switch to a firmer shift, not the racing type of tune/shift points
warm idle is around 600 rpm
new GM flexplate
I spun the torque converter several times to make sure it was seated all the way in to the pump
no clunk or harsh egagement either when cold ( high idle) or warm

Now, when I drive the car, occasionally I get a drivetrain clunk ( seems to be coming from the front of the tranny) when I let off the gas or get back on the gas. Doesnt happen all the time and it didnt do this before the swap/tune. I tried driving in 3rd, eliminate torque converter lockup, and I still get the noise, but not as bad.
So is it time for a trip to the local tranny shop, maybe have the PCM retuned back to stock shift points or is the engine too much for a stock 4l60e?

 

The "new poly engine and transmission mounts" is the red flag.
There are dozens of threads here where the OP reported various clunks and vibrations, and upon replacing the poly trans mount with a stock mount, it was all quiet again.

Do you know if the trans is shifting when you hear the clunk?

 

Not sure, but I feel it is not, Just letting off the gas and then back on the gas while maintaining a reasonably constant speed. Swapping out the tranny mount is an easy test. Forgot to mention that I also added a poly torque arm mount.

 

Well, I finally had time to replace the tranny mount with a stock style rubber mount. If I hadnt done the work myself, I wouldnt have believed the results. The heavy clunk is gone, still have a bit of a clunk at the rear differential, but that is probably the differential needing adjustment. An added benefit is that the heavy exhaust vibrating/throbbing is mostly gone as well. Have to think about replacing the poly motor mounts over the winter. Thanks for the tip!