Alternator/generator/regulator problems of the 2004 BMW 325

At around 20k miles, the smg (sequential manual gearbox w/ paddle shifters) on my '04 325ci began experiencing many of the same problems that I've read about regarding the automatic transmission. After a cold night, the smg would not shift into reverse or drive. It would keep "clunking" over and over, continually louder, until I shifted back into neutral. I had the car towed to BMW, where they had to replace the tranny. At 83k miles, I'm starting to notice some of the same problems again. Additionally, with both trannys, the car delays its acceleration for about a second or two when starting from a stop. This has always been a problem. On top of that, my alternator just went out after a cold night. In my opinion, BMW's (at least mine) do not like the cold!.