Start with checking for diagnostic codes stored in the ECU, inspect for cracks or holes in the intake piping and couplers, inspect the vacuum line which runs to the MAP sensor and check the wiring for the knock sensors.
You'll need to get a hold of the TSRM and wiring diagrams for the 1JZ sooner than later. I don't recall if anyone's even posted them here but over at SupraMania they've got a section specifically for swaps.
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