The wiring of the well is covered by the NEC and it is required to be inspected for compliance with the MEC (Michigan Electrical Code). Part 8 Rules. Rule #80.19. You should have gotten a copy of the Part 8 Rules when you took your Code Update Class as it was required by law that the class provider issue you one. As for who can obtain an electrical permit for a water well pump look at look at 80.19.1 and see that a homeowner, an electrical contractor or a well installer can obtain a permit.
If you don't have a Part 8 Rules document you can download it from the State free.