"Did not meet requirements; missing migrations" error
You don't describe precisely how you're doing your custom migration, but the key to missing requirements on migrations you are omitting is to remove the dependencies. The migration that is complaining will have in its configuration something like

migration_dependencies:
  required:
    - d6_user
    - d6_node_type
    - d6_node_settings
    - d6_filter_format
  optional:
    - d6_field_instance_widget_settings
    - d6_field_formatter_settings
    - d6_upload_field_instance


Simply remove references to migrations which you are not running.