The Department may adopt rules and regulations that relate to application for, issuance of, revocation of, or modification of discharge permits. The rules and regulations may require submission of plans, specifications, and other information. Subject to subsection (c)(2) of this section, the rules and regulations adopted under this section shall set a reasonable application fee in an amount designed to cover the cost of the permit procedure. Subject to paragraph (2) of this subsection, the rules and regulations adopted under this section shall set a reasonable permit fee schedule for industrial users based on: The anticipated cost of monitoring and regulating the permitted facility; The flow of effluent discharge from the permitted facility; and The anticipated needs for program development activities that relate to management of the discharge of pollutants into the waters of this State. The Department shall charge a one–time permit application fee of at least $2,000 on receipt of a notice of intent to seek coverage under a CAFO Discharge permit for: A proposed new CAFO that will have a house capacity of 350,000 square feet or more; or Modification of an existing CAFO to expand the house capacity to 350,000 square feet or more. The Department shall charge an annual fee of at least $1,200 for the continued coverage under a CAFO Discharge permit of a CAFO with a house capacity of 350,000 square feet or more. In adopting the rules and regulations under this subsection, the Department shall consult with industry and provide that the permit fee not exceed a certain dollar amount. The Department may not waive the fee for a CAFO Discharge permit.