Smoke tested?
If you are 110% confident that you have no airleaks (not that I don't believe you but I can count the number of leak free cars that have come through Bills on my hand) then you will have to look at logging in VCDS to see whats going on...
As for the CTS... you need to understand why this 'may' be causing an issue... a faulty CTS could under read so the ECU thinks coolant temps are lower than they actually are and still be in cold start/warm up mode... this will make the AFR run rich and subsequently cause issues with how the engine runs..
Logging coolant temps when the engine is obviously warm should confirm this... else you will need to check fuel trims and see if there is any excessive adaptions that could indicate an airleak
Other possible candidates are MAF, O2 sensor, injectors, plugs etc... you just to be systematic and ideally have VCDS (or something thats at least capable as most stuff varies wildly in capability) to hand to be able to see what the ECU is seeing
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