it is not. most manual 4AFE use 26-16-12 pins on the ecu and the automatic ones use 26-16-22 pin ecus so while the pin names are relatively the same, their pin locations are different
I myself use a manual 5AFE engine but use a 3SFE A/T ecu from a JDM ST191 Caldina.... no problems there, I just had to use an ecu adaptor to connect the 3SFE ecu to my 5AFE manual harness and make it work properly.