The thunk happened on the 3-2 downshift. I've looked at the flex discs and they are intact with no cracks.
I played with the modulator increasing the pressure by turning it clockwise 2 full turns. It seems to have helped it. I also made sure the modulator is holding vacuum. I've driven it a while intentionally trying to reproduce the "thunk" and it has only happened once under full throttle coming out of a turn. Driving normally has not caused it to happen. The shifts are slightly firmer, but not harsh.
I'll continue to observe and report back.