Sounds like a possibility is the misadjusted throttle linkage. This probably caused a higher than normal ATF line pressure which resulted in rough shifts for all gears.
Can you take a picture of the cables at the throttle body?
Look at message #43 here, you should see 0-1mm of the cable stake out of the rubber boot when the throttle is fully closed. Toyota uses a throttle plate opener to prop the plate slighly open, so you'll have to manually close it by turning/pressing on that round wheel thing.
'00 5s-fe loose throttle valve cable, how is yours ?