If the Agency refuses to grant or grants with conditions a permit under Section 39 of the Act, the applicant may, within 35 days after the date on which the Agency served its decision on the applicant, petition for a hearing before the Board to contest the decision of the Agency [415 ILCS 5/40(a)(1)]. The petition must be filed, and the proceeding conducted, pursuant to the procedures of Section 40 of the Act and Board rules at 35 Ill. Adm. Code 101 and 105.