Electrical issues, probably more than coincedence

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cleatus

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eastern NC
My sons 98 expedition, 4.6 4x4 od light started flashing. About the same time the power windows started blowing it's fuse. I took it to the transmission shop. They rebuilt the trans about 4 or 5 months ago. The code that showed up was the trans output speed limiter. They cleared the code everything seemed fine. A few days later the light was on again. Took it back and they found the trans wiring harness on the exhaust. Their fault but since they couldn't or wouldn't be able to get right on it I told them I would check things out. I repaired the harness today. 3 wires had the insulation melted with two bare wires stuck together. The copper wires were intact and the copper was still shiny with very little cleaning. I taped the wires up, reinsulated them and rerouted them. The job wasn't nearly as bad as I thought and didn't take much time. I unplugged the battery for some time during the job and again for sometime afterwards. The truck still blows the 14 fuse , battery saver ( never helped for a battery drain), interior light relay, and power windows. My son drove the truck a while, the light didn't come on, but when he went to restart it later, the light came on. I'm going to replace the output speed sensor and hope that will that but still not sure what could be causing the fuse to blow. When the windows quit working I unplugged the windows motors and plugged them in one at a time and could n't get the fuse to blow. Went to start the vehicle the next day and boom, there goes the fuse. Could this be a bad GEM? No doubt the wiring harness needed repair. The 4wd has been finicky engaging lately also. Trying to get some feedback before I just start throwing money at it.
 
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