Think it could have anything to do with the Vehicle Speed Sensor or the electrical connectors near it getting wet? The VSS is located on the passenger side of the transfer case and there are a couple of electrical plugs right in that area. The VSS also provides one of the electrical inputs to the PCM.

I know I'm not the only person here who's ever had those connectors get wet and had the engine start running very rough anyway. The time it happened to my VX was when I was driving in a very hard rain on the highway.

The one's I'm talking about are near the rear passenger side of the transfer case, and for some reason I remember having to remove the transfer case support cross-member, so there may be another part of the wiring harness routed along the top of the cross member. I ended up drying the connectors, coating them with dielectric grease, and adding some heat-shrink tubing to try to waterproof them as good as I could, and haven't had any similar problems since then.