Wow... Everytime I read the threads you start, its as if I started it. Same noises, same vibrations, and same everything if I had those damn gunmetal 87's! Where the hell did you find those anyway?
Since I know exactly how you frustrated you are trying diagnose your problems:
I have the same noise on a cold start up. It lasts for a second or so immediately after starting. I gave up after countless hours of research with no solid answer. What I found was that its caused by the VANOS and doesn't seem to be a major concern or high priority repair. It sounds wierd buy try searching for "marble(s)" here and bimmerforums.com
http://www.xoutpost.com/bmw-sav-foru...ed-fixing.html
this link is embedded in the above thread:
http://forums.bimmerforums.com/forum/showthread.php?t=1041320
What I have found is that this knock on start up seems to be how my X tells me that it needs an oil change. Its not low or anything, just time for fresh lube.... I change my oil very frequently because when I went to change my oil filter for the first time, I found that there wasn't one. hahaha... what else to do but laugh and flush it. It was completely desolved and turned into a sludgy muddy paste. Knock on wood but I have no leaks, no shakes, no power loss, and no knocks other than the occasional marble clack on start up.
Changed the oil and problem solved every time. Noise comes back usually around 3 or 4 thousand miles
Unfortunately I just became a member of the 6 digit mileage club.
I stumbled across the thread below looking for the link above for you. I have no idea what this guy is talking about or how a rubber bushing can make an engine knock but I thought you might wanna take a look?
http://www.xoutpost.com/bmw-sav-foru...can-sound.html
Completely wrong thread, but did you ever replace your flex discs?