Since the Floppy Emu works, as well as the external 800K drive, I don't think there's a problem with the Bourns filter.

If I'm understanding correctly, you have one internal floppy mechanism that can't read nor eject disks, but other external disks work OK? Have you tried taking the floppy drive mechanism out of your external 800K drive, and putting it inside your Mac as a new internal drive?