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I know it's been a long time since I asked the question, but I just wanted to post a quick update and thank the guys who helped me again.
The truck is officially on the road again, and is running like a champ. I found the shorts, replaced the starter and some wiring, and now the truck is running like new.
Where did you find your short at if I may ask? I'm having a a very similar issue. The fusable link to the alternator is fried. That was an easy fix. I had a pair of jumper cables go up in smoke on me last night after I changed that wire.
I didnt have this issue until after I put an aftermarket floor shifter in.
My advice: trace all of the major wires and cables before starting on the small wires. It turned out to be something simple, but I jumped to conclusions, and assumed that the wiring harness itself was shorted.
im going to start tracing from the solenoid when I get off work today....im thinking it may be something that runs under the cab since i replaced clutch and put in the shift kit.