Re: Agree with the other posts, but consider this (archive)

it's possible that the car was improperly towed, but make sure the new altn. is putting out the correct voltage, not too high and not too low.
BMW transmission control units and the ABS ECUs are very, very sensitive to power and grounds.
Too high of an input voltage and they go goofy, or just fry on the earlier cars. Later vehicles had protection built-in just for this, and would even set "Check Engine" light faults to warn you of a major electrical problem via the voltage regulator of the Altn.

Also make sure that the throttle position sensor or the throttle setting hasn't been played with. That one sensor only runs with a 0-to roughly 4.76 volt scale, any moving of it or the throttle plate in an attempt to correct idle speed of the engine can throw the shifting of the trans off completely! Lots of techs don't know it's lurking under the big black boot on the side of the throttle. Once someone plays with the 10mm nut and levers at the other end with an attempt for idle speed raising, you have to recheck and usually reset the "pot" of the trans potentiometer. BMW has very strict voltage settings for either at idle or full open to be met.

Lastly, the altn has to put out a "clean" amount of power. Rarely, you'll run into a "dirty" output, with poor performance of the diode pack or another internal part. Usually a result of a poor rebuild unit, or one that needed new guts.
If you view the signal on a "scope", you'll seen a bad wave pattern that shows the "dirty" signal.
This can loop up an ECU.

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