Are you using the HKS adaptor harness?
From my understanding, the Kurofune doesn't support DBW, so the stock JZX110 ecu must remain to control factory DBW. Alternatively, there are kits which manualise the throttle on JZX110s, essentially making the E-throttle redundant.
Personally, my planned ECU choice for my JZX110 is an Altezza link. Connecting the Altezza link to the JZX110 harness is either by re-pinning the JZX110 ecu plugs, or making an adaptor harness. I'm in the process of making an adaptor harness. The stock DBW should remain functional as the Altezza link supports it.