== Resolution Update ==
The rough running was solved by installing an Autozone 94R-DLG. Battery light no longer shows and the car runs very smooth after cold starts now + the transmission no longer makes really rough changes in the first few miles.
Dealer attempted to fix using the part numbers which made no difference:
New Battery cable, negative, IBS (12427603567 $ 217.24)
New Adapter for IBS (12517615476 $52.37)
New Adapter lead IBS (61129123571 $13.27)
The original battery would show green in its eye after being charged with a CTEK. Typically it would run fine on the next start but then be back to square one with the eye showing black.
Six Euro Deliveries since December 1998 (Owned E46, E90, E91, E92 and E93)
28 vehicles in 26 years of driving so far. Guess I like cars
Last edited by MP3_E46; 12-29-2012 at 03:52 AM.