What I understood from your message is as follows. Are these correct??
1. Your vehicle is HR30 with L20ET mounted.
2. You have got your original ECU failed for some reason and needed to search for the replacement.
3. You found an alternative ECU from a twin-turbo FJ20 vehicle.
4. You had it connected with your L20ET by hot-wiring and managed to get it started.
5. You however encountered a problem that ideling speed stays as high as 1300-1500rpm even when running on the road.
If all the above points are correct, I would suggest you to...
1. Check if the water temperature sensor is properly wired and connected with ECU.
2. Make sure that there is no imperfect connections between pipes/hoses allowing air coming into engine.
HOWEVER, in a first place, for me, the word "twin-turbo" implies that the air/fuel ratio of the ECU you found has already been far- differently set from factory-original one.
This may be the point where you should start to check.
Hoping this helps. If not, post here again.