I just had the same issue last week with my 2005 Freestar Sport. I got the van from family and knew it had some history of this problem. The mechanics my parents took it to thought they had is solved. Apparently not.
Here is what I discovered. First, one of my PCM mount brackets had broken. This did not allow the cover to seal to the firewall. They tried with silicon and a bag over the computer. Bag was useless and ripped before the cover was on. I fixed that by installing two self tapping bolts above and below the previous hole. Cover seals tight to firewall now.
Second, my cover had a crack and a hole on the top of it. Real easy for water to get in. I had a cover lying around from a 98 Windstar, identical and same part number. Crack and hole gone.
Third, and probably the reason for the mystery of where the water is coming from. When my computer was out, I felt in with my hand and there was water on the chassis directly above the PCM. Looking through the glove box area you can see a plastic cover over a stamping hole that is sealed in place (obviously not anymore). There was some evidence of water leakage out of this area and down to the PCM. Investigation revealed that there is an enclosed cavity (a boxed structure element that runs the width of the vehicle under the windshield. Water is getting into this cavity, accumulating and eventually getting down onto the PCM.
I found a TSB for a 2006 Freestar that describes installing a deflector under the lower cowl to route water away from the PCM cover in the engine bay. 3/4 through that TSB it says to remove two rubber grommets. I believe these grommets provide a drain for the enclosed cavity. Mine both had rust scale on them.
I also discovered that water gets in this cavity from the clips that hold the upper cowl cover (6 or 7 along the base of the windshield). If they lose their factory seal (through aging most likely) water gets in and has no where to get out. Eventually it does.
I just repaired it this past weekend so time will tell if I have solved the issue. Everything makes sense that it is better now but we will see.
Monday, September 12th, 2011 AT 6:58 PM