600 +/- 50 RPM is the
initial target when adjusting idle speed in the idle set up procedure with the SCS shorted. Once the SCS short is removed and you raise the RPM to 1000 RPM briefly the idle speed is supposed to stabilize at 800 +/- 50 RPM as the final step in the procedure. So, your idle speed of 600 RPM while stable, is abnormally low. However, if you are estimating speed based upon your tach, your tach could also be out of calibration (a common problem). If you have access to an OBDII scanner (or scanner app and dongle), a good one should be able to display the engine RPM that the ECU is measuring and confirm whether the RPM is correct or incorrect.
The
recommend iac valve inspection and flush coolant." Both were done later but problem persisted.
action by the dealer is a bit of a mystery since there is no iac valve to inspect. That is a conversation that you may or may not want to have with the dealer.
If you confirm that your idle is stabilizing at 600 RPM, that is too low and will always create a problem for maintaining a smooth idle. However, I am going to speculate that if the ECU is not getting the correct signals from the brake switch, the clutch switch or the transmission neutral switch, it may not be possible to successfully take the ECU through the idle setting procedure. The service manual procedure does specify that the transmission must be in neutral when carrying out the procedure.
With the clutch engaged (pedal up) and transmission in neutral, the ECU needs the 'neutral' signal from the ECU to tell it to go into idle control mode. When you are in gear; but, stopped with the clutch pedal pressed to the floor the clutch switch gives a signal to the ECU to put it into idle control. So, just guessing that because the idle stabilizes with the clutch pedal pressed down, the ECU is getting the signal from the clutch pedal. When you let the clutch pedal up with the transmission in neutral the signal from the clutch pedal disappears; but, should be replaced by the signal from the transmission that the car is in neutral so it stays in idle control mode. If you let the clutch pedal up and there is no neutral signal from the transmission then the ECU assumes that the car is in gear, clutch is engaged and you should be pressing the gas to go forward - hence no idle control. So, based upon your symptoms my first guess would be that something is up with the neutral switch signal. You can test for the neutral switch signal using the procedure in the service manual. As an observation, since the transmission came off when the clutch was replaced, the neutral switch had to be disconnected. Its possible that they completely forgot to connect the neutral switch during the re installation, or that the plug is not completely inserted in the switch or that it got buggered up some how. So as a first step visually check the neutral switch. If it appears OK then the next step would be to check the signal, including the brake pedal and clutch pedal signals at the ECU as set out in the service manual.
The idle setting screw on top of the throttle body allows a small amount of air to by-pass the throttle plate and this is what sets the base idle speed of the engine. Air is admitted to this system by a port upstream of the throttle plate. It is possible that 'something' has gotten in there and is buggering up the air flow for the base idle setting. However, this port is upstream of the throttle plate and normally doesn't get exposed to products from the PCV and EGR systems so should stay clean, particularly if you are using the OEM paper air filter. You could give this port a shot with some throttle body cleaner using a straw in the port if you are inclined; but, I don't think it is the problem. Also, the dealer probably did this as part of their service attempt.
In summary, you could have two problems. Missing signal(s) to the ECU and a base idle that is too low. I think you need to check for the missing signals first before trying to set the idle speed.
A light flywheel does not help the problem; but, I would be extremely surprised if it is causing the radical idle problems you are describing.