Pump all the water out of the basement and away from the furnace with a submersible pump. Run the pump outlet pipe outside of the house, where the water can drain. Turn all gas shutoffs on the furnace to the off position to prevent a gas leak.
Loosen the gas supply line with an adjustable wrench. Turn the line counterclockwise to remove it, and repeat the process for the pilot line, main burner line and the thermocouple. Locate the burner assembly on the furnace and pull it out of the chamber. Clean the inside of the burner assembly to remove any dust and debris that may have accumulated there during the flood. Wipe it clean with rags and blow out the assembly with an air hose.
Clean the vent screen on the blower burner with a rag to ensure it is free of debris. Set the burner assembly back in place and attach it securely to the furnace. Blow out all the ports on the control unit with an air hose until there is no water remaining.
Attach the pilot line, thermocouple and burner line by turning them clockwise in place with an adjustable wrench. Do not overtighten lines, which can strip easily. Reconnect the gas supply line. Turn the gas supply line on at the valve. Mix 75 percent water with 25 percent dish soap. Pour some on the valve and see if it bubbles around the fittings. If it does there is a leak.
Shut off the gas, disconnect the leaking fitting, wrap the pipe threads in Teflon tape and reconnect the fitting. Turn on the gas and check again for leaks. If the fitting is secure, light the pilot light underneath the furnace with a lighter or match to turn it on and make sure the furnace is working properly.