You probably have water trapped in the connectors of the engine harness.
They will dry out eventually but may leave deposits in the connector which will cause corrosion and bad connections.
I would recommend that you get a can of "Water Displacer 40", disconnect every electrical plug on the engine harness, and flood with the WD40.
Major targets would be C109, the TPS, the CPS, the CTS, The main and fuel pump relay sockets,the ICV plug.
You may also want to disconnect the fuel injector plugs and clear the water out of them.
Don't forget to dry out the distributor cap/rotor with a clean dry rag only...no sprays.