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I don't think the JZX90 needs an extension either. AFAIK, JZX90 and JZX100 both use the R154 with the external tripod shifter. Neither of them should need the housings swapped to fit an sc300. If anyone has more solid info on this please feel free to correct me.
Can't really do much from here since I don't have a Chaser wiring diagram or ecu pinout. You may end up having to just "Chase" (Hah!) everything out manually and cross reference everything on the SC harness to figure it out. Hopefully someone here has the proper documentation and can provide a bit more help.