Clean Energy for America Act This bill amends the Internal Revenue Code to modify or replace several existing energy-related tax incentives to provide consolidated tax deductions and credits for the production of or investment in clean electricity, the production of clean transportation fuels, and energy efficient homes and commercial buildings. The new tax incentives are technology-neutral and the amounts of the credits or deductions vary based on the levels of carbon emissions for the incentives for electricity and fuels or energy efficiency in the case of the incentives for energy efficient homes and commercial buildings. The bill also establishes tax credits for certain bonds issued by a governmental body, a public power provider, or a cooperative electric company for facilities producing clean electricity or clean transportation fuels. The bill phases out the new tax incentives when annual greenhouse gas emissions in the United States have been reduced by at least 35%. In order to provide for a transition period for the new tax incentives, the bill temporarily extends several existing energy-related tax provisions. With respect to the existing qualifying advanced energy project credit, the Department of the Treasury must establish an additional qualifying advanced energy project program to consider and award certifications for qualified investments eligible for credits.