I would take apart the main engine wiring harness connector and check for water intrusion. That is the one right in front of the driver window. Then I would check the connector at the controller to the rear of the passenger side valve cover for the same water intrusion. It sounds like that is what happened.
Make sure you use dielectric grease when you reseat the connectors.
Dave
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1999 AMGeneral H1 6.5TD BLACK Wagon e-Lockers Front and Back, Rubberduck4x4 RockTubes, Extended Undercarriage Protection,"Big Duck" 2" body lift/2 1/2" suspension lift, 41" IROK Radials on 17" Cepeks w/Rock Rims, (in process)Centered front diff, 3.08 gears, 12k Brakes and 12k halfshafts
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