Coke (or any carbonated drink) is most acidic when it is just opened. The acidity comes primarily due to phosphoric acid. Citric acid if present also adds some acidity. Carbon dioxide (which is present as dissolved form) will increase acidity though by small amount. Carbonic acid, formed upon dissolution of $CO_{2}$ is a weak acid. Its contribution to acidity, when phosphoric acid is present would be negligible.
Facts
Solubility of a gas is more in cold liquids.
Carbon dioxide dissolves in water. The dissolved $CO_{2}$ is now in equilibrium with carbonic acid. The so formed carbonic acid is much less in concentration than $CO_{2}$ itself.
Considering small effect on acidity from carbonic acid:
Just opened coke can will have higher carbonic acid (whatever be its amount), due to higher (relatively) dissolved $CO_{2}$. As temperature increases $CO_{2}$ fizzles out to air, and dissolved $CO_{2}$ is reduced so is carbonic acid.
PS- Microwaving coke can will be dangerous. There is a hazard of explosion and severely damaging your microwave oven of-course !
I am not sure if cleaning with coke will help in your situation.