1. The commission shall establish, by rule, a procedure for the orderly submission of applications for an operating permit by those regulated air contaminant sources in operation on August 28, 1992, and procedures for the issuance of operating permits. Any person who operates an air contaminant source on or after August 28, 1992, shall submit to the department, with the application, payment of a one hundred-dollar fee with the request for the approval of an operating permit.

2. Any person who wishes to construct or modify and operate any regulated air contaminant source shall submit an application to the department. The commission shall establish, by rule, procedures for the orderly submission of applications for those persons that wish to construct or modify and operate any regulated air contaminant source and procedures for the issuance of a permit to construct or modify and operate. The department shall review applications within the time period established in sections 643.075 and 643.078 or under section 502 of the federal Clean Air Act, as amended, 42 U.S.C. § 7661, as appropriate, unless an extension is requested by the applicant and approved by the director. Each applicant must obtain both a construction permit and an operating permit but the department shall establish a unified review, hearing and approval process. The holder of a valid operating permit shall have operational flexibility to make changes to any air contaminant source under the provisions of subsection 14 of section 643.078 without submitting an application for an operating permit under this section.