I went ahead and tried to re-run the script, keeping in mind the usual issues with duplicate entries for payment types. I rec'd the following note in the admin console and still see nothing for Super Orders other than in Admin --> Configuration --> Super Orders:
ERROR: Cannot ADD column date_completed because it already exists.
ERROR: Cannot ADD column date_cancelled because it already exists.
ERROR: Cannot ADD column balance_due because it already exists.
ERROR: Cannot create table customers_admin_notes because it already exists
ERROR: Cannot create table so_payments because it already exists
ERROR: Cannot create table so_payment_types because it already exists
ERROR: Cannot create table so_purchase_orders because it already exists
ERROR: Cannot create table so_refunds because it already exists
ERROR: Cannot insert configuration_key "MODULE_PAYMENT_PURCHASE_ORDER_STATUS" because it already exists
ERROR: Cannot insert configuration_key "MODULE_PAYMENT_PURCHASE_ORDER_PAYTO" because it already exists
ERROR: Cannot insert configuration_key "MODULE_PAYMENT_PURCHASE_ORDER_SORT_ORDER" because it already exists
ERROR: Cannot insert configuration_key "MODULE_PAYMENT_PURCHASE_ORDER_ZONE" because it already exists
ERROR: Cannot insert configuration_key "MODULE_PAYMENT_PURCHASE_ORDER_ORDER_STATUS_ID" because it already exists
ERROR: Cannot insert configuration_key "AUTO_STATUS_PO" because it already exists
ERROR: Cannot insert configuration_key "AUTO_STATUS_PAYMENT" because it already exists
ERROR: Cannot insert configuration_key "AUTO_STATUS_PO_PAYMENT" because it already exists
ERROR: Cannot insert configuration_key "AUTO_STATUS_REFUND" because it already exists
ERROR: Cannot insert configuration_key "AUTO_COMMENTS_PAYMENT" because it already exists
ERROR: Cannot insert configuration_key "AUTO_COMMENTS_PO_PAYMENT" because it already exists
ERROR: Cannot insert configuration_key "AUTO_COMMENTS_PO" because it already exists
ERROR: Cannot insert configuration_key "AUTO_COMMENTS_REFUND" because it already exists
ERROR: Cannot insert configuration_key "FED_TAX_ID_NUMBER" because it already exists
ERROR: Cannot insert configuration_key "STATUS_ORDER_CANCELLED" because it already exists
ERROR: Cannot insert configuration_key "STATUS_ORDER_COMPLETED" because it already exists
ERROR: Cannot insert configuration_key "STATUS_ORDER_REOPEN" because it already exists
Note: 25 statements ignored. See "upgrade_exceptions" table for additional details.