Check a wiring diagram if you have a manual. My truck is a 89 so may be different. There is a fusible link but as I recall it is from the power output on the alt to the starter soleniod. I don’t recall if there is a separate wire from the soleniod to the reg or if it splices into the fusible link. You can trace it or look at a wiring diagram. I ran a new larger gauge wire from my alt output to the solenoid as I could see the fusible link was a little dodgy and the connector at the alt was a little fried.(Overcharging or to small of a gauge wire, figured I would upgrade.) Also check your voltage at say 1,500 rpms. I have noticed they don’t seem to charge at +13 volts at idle, the voltage rather seems to go up once off idle. (Especially when started.)
A couple years back when I changed out my alt and reg I had the same result. My new issue turned out to be the ground wire for the regulator. When I was changing out the reg the following occurred. The ground wire went to a connector to another connector to ground.(Might of been one connector.). That connector was fairly corroded and moving the wiring around caused it to stop conducting power.(Probably moved to a more corroded part of the blad connector after a little tugging.) After cleaning up the connections and trying again it all worked.
To your point, due to the shorting out of positive battery cable checking, all the wires for solid connectors and continuity is in order. Hard to know what it may have damaged. Clean up all the connectors for a solid/good connection.
Also you may want to field test the alt. Sadly you no longer can assume a rebuilt or new part will work out of the box. Countless members have chased issues to find the new/rebuilt part out the box was to blame.
Here is are a couple good videos to watch that may help you out. Take some pics of you testing and post.
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Want to upgrade take a look
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