Even if the car shifts and drives smooth as butter, I should still be worried about it? I don’t mean to drag this on but as you can see im beyond worried.
Colston , assuming you have a credit card why not just have it fixed and in two weeks send that amount to the credit card company .
You are combining 2 different things. The gearshift is INSIDE the transmission and the flywheel and clutch is between the transmission and the engine. They are not related in any way.
And I would be too if it was mine, but I’m so lucky that I know not to buy a car with DM flywheels. Unfortunately not everybody else has that knowledge.
Edit:
At least You have the 1,9 liter. That engine is known over here to last a very very long time as long as You maintain it well and use the European spec engine oil. My recommendation will be - change it at 5k intervals. VW thinks different, but what do they know 
Edit - Edit: I forgot to remind You. Diesels are NOT for short trips/many coldstarts. They need to be used for longer durations when started to be able to last.