Yes you have to jumper some switches and merge devided body circuits
1ST
If you have a [1jz engine/manuel] inside of a [auto body] combination
you have to merge the body circuit the efi is devided into two halves the black/white wire needs to be put together with the black/blue wire because the body circuit is normaly devided into two halves with the auto body setup so the car will only start in the park postition position the NSW switch is on the efi side. please refer to the Male B1 connector pins 5 & 10!
2nd
if you use [1jz engine/auto] inside of a [manuel body] with a [1jz ecu/auto]
You have to jumper a clutch nsw switch at the ecu there is not clutch or clutch nsw switch in an autobody.
3rd if you have a [1jz engine/manuel] inside of a [manuel body] with a [1jz ecu/auto] you have to add a wire plugging into the ecu because the efi harness for for a manuel is diffrent then the efi harness for an auto you have to add a wire going into the 1jz ecu at the T connector pin 22 because the manuel 1jz manuel normaly doesntot have a wire going into the T connector at pin 22 and the auto ecu needs a signal called "22 - NSW - Start Control From AM1
here look at the diagram
Auto ECU's have a diffrent tuning they are slightly detuned to allow the auto shift smoother and to help the auto transmission last longer. They tend to also do soft fuel cuts when sending/recieving solenoid signals to shift.