The council shall, within ninety days following the public hearing, certify in writing that the application is approved as submitted, approved subject to modifications, or denied. Moreover, no city council vote to adopt, amend or deny a special permit required by this section shall take place until after the site plan review has submitted its recommendations to the city council. If the council fails to issue its findings within ninety days, the special permit shall be deemed approved. However, no building permit shall be issued until the plan, signed by the city clerk, is recorded in the registry of deeds.