Here is my issue, a manual_stepper cannot be synced to a extruder because only extruder_steppers or extruders can be synced. But extruder_steppers cant have endstops so i cant manually move it to the endpoint before syncing it up with the extruder.
Sorry. I missed that part in your original post.
For a 3DChameleon-style design, I think you should have one manual_stepper for the selector and one extruder_stepper for the drive motor. The selector can be homed with a virtual/physical endstop, and the drive motor can be synced/desynced with your extruder as needed.
Also, you can manually move an extruder_stepper. See this forum post.