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Your symptoms sound a little like a failing clutch slave/master cylinder. Have you noticed any sponginess in the clutch pedal, as well as long clutch pedal travel and grinding of gears? Have you noticed any hydraulic fluid under the car? Definitely try not to drive the car until you can get it looked at properly.

Myself and some other members have had problems with shifting into 2nd gear, especially when cold. For me, replacing the tranny fluid seemed to help for a little while, but it eventually became hard to shift again when cold. Recently, my differential input flange failed and had to be replaced. For some reason, this seems to have fixed my shift problem. The part is really cheap, so if you have this problem, it might be worth it to replace the flange. Perhaps as the flange gets old, it allows play in the entire driveline that makes it difficult to shift into 2nd gear? Also, before the flange was replaced, I noticed a rattling sound from underneath the car when going over speed bumps at a very slow speed, out of gear, and clutch pedal pressed in. I no longer hear this sound.

My indy told me that the input flange is also a problem with the M3 (don't know if this is true or not), but I seem to recall a post re: driveline/differential clunk in the M3 when I did a search for my clunking sound. That post dismissed the sound saying it's "normal" and that it's a result of driveline slack. Perhaps the flange does this in the M3 and M5 as it gets old and loosens up?
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