Just musing over the issues here I wonder if the running in noise is not due to inaccurate shimming, which is inexcusable, but insufficient lapping in of the c/w and pinion gear teeth. This would explain the noise on a new box slowly subsiding.
I remember reading about a cammy (OHC) Velocette rebuild. The owner had fitted new helical gears to the camshaft drive. On starting up the gear noise was terrible. He then built an electrically driven rig for the gears at work, and when the boss wasn't looking ran it for several days under his bench with a mildly abrasive lubricant, until the gears became quiet. Re-fitted to engine and no further issues.
Richard,
To take your thoughts a bit further, maybe that's the black goo that was in all the early, maybe later BB's too. If it was a slight lapping and lube mix, that would explain the dark color and thickening.
But if that were the case, they should have informed all the owners to run in the BB lube for 1k miles and then flush and fill back up with normal lube.
But to leave that crap in there was inexcusable. I also remember a member in TX that had his BB seize up while his wife was taking her first drive. I believe it seized at around 60 mph. I'm sure that BB was just dry as a popcorn fart...
I'm really glad that the newer M3W's are coming in a lot quieter than days of old. Sounds like MMC is doing something right.