I'm also trying here with a problem on an Octavia III - 2014- 1.6TDI 110cp.
I will try to detail as much as possible, someone may have hit the problem and can give me some advice.
I bought a car in August at 160,000 km. After about a month, the spark plug from the piston 3, the one with the sensor was broken. I went with it for about 2-3 weeks and I replaced it.
About a month or two, from time to time at the traffic light began to shake a bit at idle. At the next traffic light, maximum 2 traffic lights trepidation disappeared.
I changed the oil, filters, and as a result of another ventilation problem I went to the Skoda representative and I also made a ramp + tester check but nothing found.
I ll try to define 3 states of the problem : 1.Runs flawlessly / 2.Has some oscilations,does not run round / 3.Has severe oscilations , engine runnig verry bad, with +/- 100 rpms, seems like trying to stop and so on
After 24 hours, the car started to show the following symptoms:
- In the morning, it starts and goes flawlessly ( state 1), driving in the city for like 2 hours it goes to state 2.Having an hour or 2 parked - it goes to state 3.The next morning is state 1 again...and history repeating.
- I went again to another service, in the morning they tested the injectors and they were in normal values (state 1). Returned when it was in state 2, there were high values on an injector (+1.6), given down, taken to the cleaning. The bench test gave them normal values, changed the filter, cleaned the gallery and regulator.
- After cleaning injectors it started to do it again.
- There is also a CLANC that comes from behind the board at 1100 rpm. It looks like something plastic, a kind of flap that does not open / close.
- 4th service check, and still no answer, but found new thing...it went from state 3 to state 2 after 100km highway drive.
The great mystery is why you do it only after you go with it and take a break. I tend to think that it would be a piece that is thermally sensitive, belt, roll something.

Thanks

https://youtu.be/AwkxSKu9uoE

You say your car is a diesel so they dont have spark plugs. They have glow plugs so I would presume that is what you mean.

Is your car fitted with a dpf and the increase in revs a regen on the dpf. I know mk mk2 VRS TDi was very lumpy when doing a regen.

Diesel with high-ish miles. Lots of things to check. Problem with sticky EGR flap? 

Might be..that s my next option.

Today I replaced the alternator tensinon pulley and beld, also checked the alternator crankshaft (was ok).

I told the guy about that "clanc" at 1100 rpms and he played with the tester and forced the clap to open or close and it was the same sound.

After he played with it , i drove the car for like 2 and half hours and it was just perfect..took a brake of 30 mins and it is back to shacking and lumpy running ( about 30-40% of what it was before, but still there).

Is there a way to clean or what to do?

Thanks