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the two "clicks" you hear audibly mirror the "reset", so if you hear them both? it's "reset".
i actually had to r&r my tb a few years back, though i i can't recall exactly what the symptoms were. but there were codes. you may need to actually replace the tb, in order to rule it in/out.
Whenever the turbos are off my car the tech always replaces the metal o-rings that seal the turbo the exhaust manifold. I mention this because you referred to some loose exhaust fasteners.
You are the first person I know to have observed the TB butterfly valve during a calibration operation. Without ever observing this myself I would be willing to risk the opinion that what you saw is normal and appropriate.
I hope I'm wrong but I believe what will happen is you will put the car back together and some codes, those related to the throttle body, will come back. There are exceptions but I believe you will find this assembly is bad and no amount of cleaning will fix it. If it were dirty enough to be affected by the dirt I think you would have posted a pic of one gunked up throttle body.
Never ever touch the throttle body when it's calibrating. Also you need to disconnect the electrical to the throttle body or you will ruin the motor when moving it in and out. Great way to snap your finger.
I am having the EXACTLY same issue last night, car was rare to be driven in this couple months.
I tried reset throttle, code clear using durametric, it was fine for 10km. Cool down and going home and the symptom is coming back and car has to be on tow finally, from throttle no response to it cant be started.
So should I look into the fuel pump then? Fuel filter was replace an year ago,