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I worked in tech support and training for a car manufacturer, not BMW. Misfire counters climbing but not setting misfire codes, often it will set p0300 (can't recite the BMW hex code for this). This problem is a post engine R&R or trans R&R related in majority of cases. Anyway, it is irregularities with crank position sensor system. The aperture surface of flex plate (flywheel) has little tolerance for runout. It is easy to dent them in handling engine and mating to trans. The misfire detection is using the rhythm of slowing and accelerating of crankshaft for compression followed by combustion as it sees peak to peak periods. There can also be suppression problems when the trans to engine surfaces are dirty/greasy as aluminum is a poor shield for magnetic field anomalies. dirty bell housing disease usually shows as long cranking together with anything else as the starter throws some serious magnetic flux lines across the flex plate. The learning of flywheel irregularities, ones that can be adapted for, is usually accomplished by coast downs. You can manually select 1st and then get to 15kph and then lift throttle and let engine speed drop as speed drops to 1000 RPM or lower and then gently accelerate again to 15 KPH. Repeat 6 times and then see if misfire counters stop increasing and the roughness goes away. I do not believe there is a place to see the aperture surface (the flex plate edge ring with all the rectangular openings and a spot with no aperture) and checking for depth to surface to see if it has dent(s) would be tough but possible.
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