only when idling, when the choke is on and when the air conditioning is on
From this quote, I believe this most noticeable when the car is cold started? choke is on?
If the miss is there at idle, remove and reconnect each ignition coil power plug and observe the idle quality and RPM. There may be one coil that makes no change to the idle quality. If you can get no variation, this can be the faulty cylinder. If accessible, then you can swap 3 plug/coils about without too much trouble to localize the fault - coil or plug. Regrettably the other three coils require lifting the manifold to swap them around.
If you think it may be a vacuum leak, one way to find the leak is to blow cigarette smoke into the inlet manifold and look for any smoke plumes. An old method I used with carbureted cars was to get the garden hose and thoroughly wet/spray around the inlet manifold and listen/look for engine idle to deteriorate. Moisture on the spark plugs' gaps definitely causes a miss. The engines weren't V configuration, so the valley area being flooded was not an issue. Don't know if the alloytec can take this treatment. Should be able to?
Block the small flexible hose at the rear of the inlet manifold which goes to the one way valve which then goes into the firewall and then the vacuum tank.
Is the diaphragm in the heater tap leaking? This is managed by the console on the dash but is worth a cross-check. The hot water valve is operated when the air con is operational. The temperature of the cabin air is set by a vane system which mixes heater air and refrigerated air from the AC system.
Are your power brakes OK? Check the hose to the brake booster is not cracked under the hose clamps or loose fitting at the inlet manifold or the booster unit. If you have a slight leak in the diaphragm area of the power brake unit this will allow air into the manifold. With the engine off, try your brake pedal action you can sense when the vacuum tank has been exhausted. After the engine has run, turn off. Try to remove the connector into the vacuum tank. If it is very hard to remove, then the one-way valve and seal is maintaining tank vacuum. The rubber gasket between the one-way valve and the vacuum tank body can be cracked/split allowing an air leak. There may still be a diaphragm leak when the pedal is pushed. Block off the hose at the inlet manifold as a final check.
Have you tried a vacuum gauge on the inlet manifold. Closing off the PCV hose inlet to the inlet manifold should give some indication of the PCV operation.
Also the evap solenoid valve should not click on a cold start for about a minute. The common fault is the very poor quality rubber connector to the inlet manifold near the throttle body. You can block this connector behind the throttle body as a final check. The quick connects at the evap solenoid can sometimes be damaged by repeated connection without using any lubrication and allow an air leak.
Is the barometric pressure sensor OK. I've never had it out, but does it have any path which could allow air to leak into the manifold? I don't think your alloytec is an SV6, so the moving vane actuator assembly should not be leaking air into the manifold.
The manifold gasket should be the new type metal/rubber seal type - not the original paper? If this has been damaged through a few removals, it is possibly past its use by date and requires replacement.
This next suggestion takes the problem up a notch.
It could also be a faulty fuel injector/coil ECU circuitry. Can you get a long piece of dowel 8mm of 10mm diameter organized and listen to each injector clicking with a regular rhythm? You can navigate the dowel through to the fuel injector body under the inlet manifold. The click is quite positive.
My poor idle/miss ended up being the ECU not switching on the #4 fuel injector. The only real fix was replacement of the ECU. It took weeks to track down and was only found when the ECU totally failed in the #4 injector circuitry. At no stage did I get any dash messages SVS/safe mode etc. etc. The Tech2 memory showed the #4 injector was not working properly. The motor just idled and ran badly occasionally.
An observation - Tech2 has a memory for all past events, DTCs, unless it has been cleared. I understand that the after market analysers don't necessarily show past DTCs or possibly don't even "log/see" some DTCs depending on their "total" compatibility with the Holden modified engine management software original designed by Bosch.
Hope this can be of assistance.