Not sure if this applies to your situation, but with my JZS147 Aristo front cut (2JZ-GTE) I kept the wiring between the ECU and engine, and ditched everything else.
Then I connected wires to a few of the pins on the ECU which normally connect to the body harness: +12v, earth, fuel pump, starter, tacho, that sort of thing. The Aristo had something like 11 electronic modules (including ABS, trac, lots of other stuff) but the ECU doesn't seem to care if they're all missing.
HTH
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