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I haven't had to ask for help for awhile but electrical is not my forte. Just swapped a motor into my 93 wrangler, got the jeep running but the voltage meter immediately drew down like the alternator was dead. With jeep running battery was reading under 9v, but when I shut it off it climbed back up to 12v. I swapped in a spare alternator, same problem. Checked fuses and both 50 amp alternator fuses are blown. Replaced fuses and cleaned battery terminal and ground connections to engine and firewall, but as soon as I connected the battery both fuses blew without even turning the engine on, which seems to rule out a controls/regulator issue which is primarily what I came up with trying to search before I posted this. So, swapped alternator, battery is new and holding charge with no draw down, and everything worked before the motor threw a connecting rod...
 

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Trace the charging line (big wire) from the alternator and make sure the insulation didn't get cut and that it's not grounding out anywhere.
 

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charging line goes right back onto the regulator on back of alternator. pulled whole wiring harness apart and the only thing i found is that the alternator is wired differently than the diagram in the repair manual. two wires coming from 50amp alternator fuses on power distribution block join together and go to a ground on the head. diagram shows 4 connections off the regulator, 2 grounds, and 2 wires that head into the harness to the ecu, with the wires from fuses going to alternator (presumably this is the charging wire?). my fuses just connect to the ground as previously mentioned and big wire on alternator goes back into regulator which only has 2 medium size wires coming out of it. trying to find charging system diagram for 93 specific. also, battery reads 12v with multimeter but dash volt meter reads 9? still don't understand how fuses could blow without running engine.
 
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