... 400k floppy drive and un-seized it. motor spins up, ejects etc. the read write head often goes right past where it should and starts clonking but I’m think it’s a rom problem and not a faulty drive.
If this is correct:
Lisa I/O Board ROMs, then the I/O Board ROM appears to correctly match your 400k drive.
The 68000 CPU doesn't directly access the floppy hardware, only the 6504 on I/O Board does so. So although the older ROMs on the CPU board incorrectly show upper and lower drives in the startup-from menu, I don't think that alone can cause the FDC to send erroneous commands to the floppy.
Also, whereas the Twiggy head stepper phase lines are controlled by the 6504 FDC (similar to an Apple ][ drive) which can result in weird drive behaviour if the I/O Board is malfunctioning, the 3.5" drives are controlled by a step in or step out signal, and IIRC the drives are smart enough to not go beyond their limit.
Hence, I suspect a problem remains with the drive itself, eg. a photo-interrupter blocked or disconnected so the the drive electronics cannot sense the head carriage position.