Welcome back:
You know, and this is a long shot, I wonder if the noise is causing an issue with the crankshaft position sensor, Think about it, if it is banging on the crankshaft via the clutch, it could be causing an erratic signal from the sensor. I have no idea if you have an oscilloscope to test the signal from the sensor. However, if you do, here are the directions and what you should expect to see. I have no idea how bad the knock is you hear, but it could even be related to the crankshaft thrust bearings which commonly wear out faster with a manual transmission. In addition to the test below, check the crankshaft at the harmonic balancer for excessive end play.
Here are the directions I mentioned. The attached pics correlate with the directions.
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2004 BMW 525 (E60) L6-2.5L (M54)
Set Oscilloscope Display Crankshaft Sensor [FUB-SOW-FIN0201SO47TU001 - V.4]
Vehicle Powertrain Management Sensors and Switches - Powertrain Management Sensors and Switches - Computers and Control Systems Crankshaft Position Sensor Testing and Inspection Oscilloscope Patterns and Waveforms Set Oscilloscope Display Crankshaft Sensor [FUB-SOW-FIN0201SO47TU001 - V.4]
SET OSCILLOSCOPE DISPLAY CRANKSHAFT SENSOR [FUB-SOW-FIN0201SO47TU001 - V.4]
Functional description
Set oscilloscope display crankshaft sensor
FUB-SOW-FIN0201SO47TU001 - V.4
Signal at idle:
Pic 1
Signal at starting speed:
pic 2
Let me know what you find
Joe
Images (Click to make bigger)
Friday, October 18th, 2019 AT 6:45 PM