So, I bought this car with harsh (thump) down**** and 1-2 2-3 upshifts that would flare (rpm jump when the transmission goes to neutral momentarily before engaging to a higher gear).
Things that I've done so far are:

1) toyota IV transmission fluid change
2) B4 piston cover updated (because it's stupidly cheap and why not try it)
3) counters reset, adaptation reset, adaptive sequence done
4) installed transmission oil cooler from 2005 Toyota tundra that I found in JY (not very happy with how it's positioned right now; might have to re-position it for more air flow and/or add a dedicated fan).

When it's balmy 75 F or so and under its shifts smoothly on highway or in heavy stop and go traffic.
When it's 85 F and over it's fine for the first 30 minutes or so of in-town driving, but after that time runs out it starts flaring and hard downshifting with a clunk when stopping at the light, takes a while to go between gear at the take-off from the light (flaring), and so on.

Next in line could be valve body or a whole transmission, but I would like to hear your comments and ideas before going there.