I presume this happened after the mounts? the small bubble in the clear filter is normal. With the engine running, crack open each hard line at the injector letting the fuel drip and the engine should drop a cylinder just like removing a plug wire from a running gas rig. As each injector hard line is opened the miss or roughness should feel the same. If, after cracking one open and the result is less than the others, then that injector is either dirty or the injector pump is the culprit. Do this after you have looked at what DIESEL911 recommends.

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81 300CD (sold) 1972 280 SEL 4.5 (sold) 1966 250 S 4 spd (sold) 1974 450 SL (sold) 86 BMW 325ES (sold), 1973 280C (sold) 1988 300 SE.