There a voltage relay on your alternater and pcm if one goes out it screws every thing up but the reason it goes out on pcm that means when u replaced the alternater the battery was connected and fried voltage relay or from sound system or changing anything that goes to pcm . My bad on spelling just rember do any work on car take battery of. My pcm took out alternater ac and trans it sucks

 

There are no relays in the charging circuit. The two field leads go directly into the pcm to regulate voltage. A bad connection can fool the pcm to overcharge the battery.