Knoking sound wile driveing it comes and goes

well it's broken and needs SERVICE
are you asking how to test and find exact cause
or asking wild guesses/?
why o why?
first are the guides inside not broken and jamming
and the motor drive there on most car for sure newer
have kid proof motor clutch that fails and slips too soon
or the the motor is weak,or bad wiring to the motor.
what I do is remove motor and operate window by hand
if ok ,make sure motor gets full 12vdc power using a voltmeter, if that is good then motor is bad.(clutch and all in one)
next you ask how ? to get to those parts?, answer pull the door cards. they pop off, google how. or youtube it.

Put foot on brake pedal

Is it a full auto box or auto with manual selection. Full auto has only 1,2,D,R. If its full auto take it to a regular tyre/exhaust place and ask them to help.
The vw and audi auto gearboxes that also have selectable manual gears are only reliable when they have the correct clean oil in them.
The oil is special and expensive, and you must only use the oil from VW. If you havent changed the gearbox oil, get it done. Its much cheaper as a first step, compared to taking the gearbox apart to check for wear or damage.

Check the oil pressure with a mechanical gauge, I think you have a low oil pressure

Sounds like they didnt bleed it out properly

Make sure there was enough oil put in and that it is not leaking through the oil drain plug or the oil filter.

No good news on this one I think
Your whining sound problem is the Layshaft bearings in the gearbox are badly worn. It also seems that the baulk rings are damaged on 5th gear.
John

sounds like a stop up ac drain tube you need to pull back carpet on wet side and look see wile car is running and ac is on
good luk hope you see some sines of water running

you need another transmission

I had the exact problem with my wifes 99 Cabrio - parked for 9 months. Ended up having to have the shop reprogram the ECU - it then worked fine.