just read this whole thread for the first time.
sounds to me like the lock-up clutch in the convertor or the spool that controls it is the cause of the dramas.
has anyone having problems with a diesel auto had the engine stall when coming to a stop after driving above 45-50 klm/hr? if so this is a symptom of the lock-up clutch not releasing and stalling the engine and this would be accompanied with the symptoms previously described ie. jerky operation in 3rd and 4th, won't kick down from 4th to 3rd or is very harsh but is fine when done manually.
the reason it is smooth when done manually is when you move the gear selector from 4th to 3rd the ecu disengages the lock-up clutch regardless, rather than try and workout wether or not to leave it locked or unlocked.
the lock-up clutch only operates in 3rd and 4th to so that is why most of the problems will be only in these gears.
my 2 cents worth