Ok, I had a similar problem on my 240d. Tranny grinding and rattling noise when the clutch was up and the car was in neutral. Drove fine. When I pressed the clutch the sound old go away. Sometimes the car wouldn't make the sound at all. Clutch up in neutral would make the noise. I could make it go away sometimes if I pumped the clutch a random number of times.

I posted it here years ago and mostly people said throw out bearing which in reality causes a clutch down whining (not what I had) or they said the German trannies just make noise.

So here is what I found.

My car had 320k and I have no idea how old the clutch was. The guy I bought it from knew how to shift so I bet it had lasted a long time. I'm very light on my clutches especially in a torquey car like my 240d that can crawl off the line without throttle. I take it most guys here know how to save their clutch so this may be your problem too. My clutch was undoubtedly old.

One day my car wouldn't go into gear. No bigs I figured it was a slave cylinder. A week later I changed slave and master and still no go. The clutch had plenty of grab before this happened so I'd didn't get it.

I dropped the trans (1982 240d 4spd) and out pops all those little coil springs. The damper thingies destructed and we're moving around in there. Plenty of meat left on the clutch. They I see the throw out. It had self destructed and collapsed. I drive so gingerly on my clutch I killed the throw out bearing first!

So you may have some damper springs moving around in there. I suspect this could be a problem on old 240d manuals because they don't have enough power to tear up the clutch and they tend to be driven by careful/skilled drivers. How else you gonna squeeze any speed out of that thing? The last thing we want to do is burn some of our precious hp making heat on the pressure plate.

Drop the trans. Or better yet, rent at borescope like stretch said and go in the slave cylinder port.

When I posted this question up several years ago a couple of others had the same issue. It was open and unresolved.

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79 300TD “Old Smokey” AKA “The Mistake” (SOLD)
82 240D stick shift 335k miles (SOLD)
82 300SD 300k miles
85 300D Turbodiesel 170k miles