Water is condensation in the exhaust and is normal. The black stuff is carbon from incomplete combustion of the fuel / air.
How do you know two cylinders are misfiring? Two paired cylinders misfiring could likely be caused by one defective ignition coil in the coil pack. GM puts a lot of electronics in their coil packs, but Chrysler coils are relatively inexpensive. If a coil is shorted, the engine computer can shut that circuit down to prevent damage to the drivers in the computer. It is possible for the problem to be caused by the computer or wiring, but the coil is more common.