your scrappie is not informed and is misguiding you. Any ATF change whether be it CVT, A/T, DSG, Powershift etc etc etc. are specced to be drained at normal operating temperature - this ensures two things, one is that the liquid is thinner and easy to flow out, the other is that any debris is suspended in the liquid and it will come out with the drain.
When you will fill fresh fluid - the temperature will drop itself as the fluid is cold - the level checking can then be done which takes literally a few minutes.
The noise you describe is the torque converter clutch dragging and the eventual failure you experienced is pointing to a seizure of the pressure supply circuit in the valve body of the transmission. In your case you bought a product for which toyota does not sell spare parts. The actual toyota service procedure from toyota literally says to replace the transmission with a brand new one from them. The old one you buy in scrap will be a hit or miss too.