Visual Inspection Time!
Get a good light, a mirror, and a bible (just kidding). First place to check is wiring between alternator and fuse box under hood. Check leads from alternator all the way to fuse box. Remove the battery completely so that you can see the wires going into the box. Three 10mm bolts hold the box to the fenderwell. Once removed, the box snaps apart so you can see the wires under the fuse panel and check for cracked/broken insulation, cut/pinched wires, or other obvious improper contact between wires/engine/body.
Beyond that, it could be about anywhere. I would suggest unplugging as many connectors as possible and try again. Keep plugging in connectors until the fuse(s) blow. That way you can identify the harness which is causing the problem and then physically trace the wires to the fault.
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