2006 ford free star when it rains the PCM gets wet and runs rough. Today it has rained for 3 days @ won't turn over. Battery is fine. Only a problem when it rains.

It appears to be a known issue. Suggestions that it is water getting into the Crankshaft Position Sensor 'waterproof' connector.

https://www.google.com/search?q=2000+Ford+F-250+7.3+dies+when+it+rains

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Hi Fred:
I'd start by checking the battery condition.
Retailers like NAPA will check them at no charge.

When the light is on have it checked for DTC'S - diagnostic trouble codes , do you know what they are ? Ignition system problem , coil's , plug wires if the vehicle has then . The check engine light code is probably for a engine misfire . Check Engine Light On

A flashing engine light usually indicates a misfire or several misfires. If the ignition components (coils, wires, distributors...) some how become exposed to moisture it is possible to get a rough running engine due to misfire(s) cause by arcking.

replace the spark plug wires

check your battery cable isnt loose

I own a 2004 LS. You didn't get water into the PCM,because of rain or anything else. The PCM is behind the glove box,only the connectors are in the engine compartment and their under the housing for the cabin filter. They won't even get wet from rain.

The battery could fail any time,after say three years,for any reason.

Don't know about warranty,ordered mine from factory in 03.

use dielectric grease from arts house!!!! :)

Check to see if the PCM could be getting wet.
I had a this problem with mine. It turned out to be the PCM would get wet when it rained or the van was washed recently. If the rubber gasket between the plastic shrowd and the windsheild does not seal on the passinger side, you could be getting water on the plug to the PCM. Then when it dries out it will run fine.
Ford knows of this problem but will do nothing to fix it. They did put out a TSB on it and how to seal it up.