If it was my car, i would be getting a remap of the stock ecu. There is much debate over using aftermarket ECU's with auto boxes in skylines, i wouldnt be taking the risk unless i was shown that the haltech has the software to retard the ignition timing on gearchange. The stock ecu has two fuel maps for low and high octane fuel,two ignition maps, closed loop, vct control, idle control and knock control.All these functions have been well developed by the factory. The only other option i would be considering is a plug in Autronic sm4, but im not sure they do it for the r34.
PS i doubt the stock ECU has s#$t itself, i just too unlikely unless there is something else we dont know about