Had a wierd short. Cause even weirder issue

So my positive battery cable melted in the little
Junction box next to the alternator melted till it grounded . I was unaware and was able to make it home no problems next morning I tried to start it runs for 2 seconds shutsoff .I fixed the short checked fuses , I have replaced the pcm and put my original tune back In and same issue . I turn the key to the run and all I get is a battery light I start it and the dash lights up as if a barely set it to run the truck shuts of then the dash shuts off 1-2 seconds afterward . I was able to get the truck to run but I have to disable the vats completely with a stock tune and before programming I have to unplug the bcm .when I unplug the bcm the dash does turn on like normal. I tried another bcm but I have same issue does anyone know what it could be?

Still need to post tune and log and more details of what you are actually working on.

What is the voltage doing during this time?