The engine loom and ecu is fairly independent of the body loom.. So binning the car loom is fine.
Don't know how far you can go with loosing wiring etc from the engine loom, iv never gone mental on an Altezza engine loom, I have chopped 50% of the wiring out the body loom and still ran and worked fine.
Let us know exactly what you want to chop before you chop it, and sure someone will confirm whether you can ditch it or not..
Should be fine to delete all the airbags, abs, etc wiring without issue.