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Do you have a voltmeter and a test light to do some electrical testing?
Make sure the connections at the alternator are clean and tight and there is no damage to any of the wiring there.
Make sure there is no corrosion at the alternator's mounting surface causing it to not be grounded.
Make sure there is no damage to the alternator's positive cable going back to the power distribution center, the connections at the PDC are clean and tight.
Make sure there are no blown fuses.
From there it will take some electrical testing to see what is going on, short of replacing parts not knowing if they're bad. If it's not charging then the problem is the alternator, wiring, or powertrain control module (PCM). PCM failures in this way aren't common but it does happen.