I would humbly suggest also remembering that we use dual mass flywheels and that they are prone or can make some strange noises with the trans in neutral and the motor at idle speed.....some make an occasional thud or thunk or sound kind of like a diesel motor...you know that rattle that diesel's make at idle. Also sometimes due to the nature of the cut of the trans gears in 1 thru 4(?) the trans makes rattling noises. Our gears are straight cut in 1 thru 4 like the old M22's & can make a bit of a racket in neutral....that is also what makes the gear noise we hear at low speeds in 1st especially.
Over at zfdoc.com there is a great Q & A section on the throw out bearing and some of the noises that it can make and some "do it yourself" tests to use. Also the Q & A section is generally devoted to our trans & it's associated parts with great tips for some simple trouble shooting.
Tom