Not sure if you are referring to the clunk issue when coming to a stop or not, but I am not experiencing any clunk whatsoever. My issue is more of a throttle lag / delay.
I did a quick search and found a similar thread actually:
https://www.lexusgxforum.com/threads/low-speed-shifting.2054/...
I wanted to comment about an issue with the low speed drivability and if your tune has fixed what I am experiencing @VF Tuner
When slowing down to a near stop then getting back on the throttle, there is a massive (nearly 2 second) delay in acceleration before the truck figures out what to do...