Had similar issue with my vvti 1jz-ge
Solution was to connect the harness as per wiring diagram. Specifically, gearbox have selector switch, with +12v input and outputs 2,l,r etc. These wires must be connected to the ecu for it to be aware of your choice.
Upon conversion, these wires are usually left unconnected by mistake. Because they run through body loom, not engine's one.
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