Clutch/throw out bearing? Transmission?

I have a 2010 jetta tdi. 6 speed manual. Few years ago had a rattle start in the transmission vicinity. I know enough about transmissions to let someone who knows what they're doing to work on it for me. Went to a local shop, was told throw out bearing. Had them replace clutch, t.o. bearing, and did solid state flywheel upgrade while in there. All was good for about 50 or 60k miles and about 4 or 5 years, rattle started again, same exact noise. Happens primarily in 1st or 2nd gear at low rpm. When was at its worst, I could also hear it in neutral with clutch pedal released. What I've been told since is that if it was a t.o. bearing it would only make noise when clutch pedal was depressed. I took to a different shop to have fixed this time, his guy said yup, t.o. bearing. Had them do same job, noise is still there. Owner tried to tell me was valve train because was diesel engine. We put on lift and listened together and confirmed was coming from (somewhere) in transmission. Anyone else have similar problem? Or know what i should do/where to go from here?