Judging by the year your KZ is, and saying your SCV is different, I'd assume you're probably from Australia? They have a different valve on there pump than the rest of the world, and the KZ engine ran in the 120 series, and even 150 series platform for some years.
If you were over fueling you would be puffing out black smoke on idle, is this the case? Whats drive-ability like? Is the engine idling where it's supposed to be? Maybe it's set too low if it idles smoothly at 800rpm? This can be adjusted on the butterfly valve area. It'll probably be hidden below your Intercooler if you have one. You can also adjust the TPS itself as it allows for sideways movement. Just back the two screws off, twist it and tighten screws back down.
If this fails, put a clear line on the return hose of the injection pump and make sure it's solid and no air bubbles are present, it could be drawing air in. Then you can go down the route of sensors. Crank position sensor would cause a rough idle. Simply unplug it, test resistance to make sure it's within range and even start it up to see if there is a difference. It will sound like a bucket of nails being shaken with the CPS removed. Make sure all connections at the pump are clean and plugged in. The two resistors at the side control the timing.
I noticed you mentioned at operating temp. So on cold start it idles fine?