I have a problem that I know is going to sound strange. I have tried to figure it out and still don't know how it's even possible. Every time it rains, I'm talking heavy downpours, our 2002 wind star has problems sitting over night. I have had to remove the back spark plugs and clear water comes out of the cylinder. Put the plugs back in and she runs like a champ until the next storm. I have told ppl about it and they look at me like I'm nuts but that's what happens. I've looked and looked and still can't figure how the hell it gets in there. Any ideas?

 

Something you might try to help isolate the area of entrance. What if you covered the top back of the engine with a piece of plastic. If that works then you are sure its getting in from the top of the engine . If it doesn't help then try covering different parts to see if you can narrow down how it is getting in there.
Sometimes you have to play detective and approach from different angles other than the obvious.

 

The garden hose can be a great diagnostic tool.

Anyway, I seriously doubt that you have rain water getting into the cylinders. At least not until you take the plugs out. I suspect you get water to the outside of the plugs.
Next time only pull the wires from the plugs and then use a rag and a chopstick to push that rag down along the plugs. Wick the water away and clear the rest with a hair dryer. Dry the caps of the wires as well.
There should be a rubber seal between the hood and the plastic cowl. If that is missing you run the risk of disabling the computer as well.

 

Our 2001 SEL (Betty) doesn't like the puddles that come with hard rains, iether. Once you hit the first long puddle, She coughs, spits and jerks until she gets home and sits and dries out for a little while. I think it's water getting around the back plugs from water being splashed (or sprayed) from underneath some how.