I picked up a C128D with a non-functioning internal 1571 disk drive. Using a copy of 1541/1571 Drive Alignment loaded from an external 1571 drive (logical drive 9), I was able to guess my way through the process, given the directions do not cover the internal 1571 of the C-128D. You can read more how-to from the manual, the closest example is the "newer" external 1571 described on page 7.
Note the 4 screws at 12 o'clock in the photo above. The two that are closer together are the stepper motor adjustment screws and they control how far back the stepper motor goes. I made minute adjustments until the program passed the Bump test with an "excellent" score. Click on image for larger view.
The Commodore C-128D "cost reduced" model running GEOS 128. The internal 1571 drive is running the GEOS interface and desktop, and the external 1571 drive contains the application program. GEOS checks for a "B" drive (drive 9) when it loads the program. Click on image for larger view.
Commodore GEOS is a pretty sophisticated GUI for an 8-bit system. The mouse is a joystick. Pictured is the opening screen of geoPaint. Click on image for larger view.