The issue came back for me too. I had come to find out my battery was too small. Replaced it with the right one. 600 cold cranking amps as opposed to the 525 I had. That's the only thing I can suggest.

 

Yeah Im not sure if it is the battery. I replaced my old battery with one of the same specs, but the old battery was in the truck when it was fully functional.

 

Update:
Replaced battery cables to starter, ground and positive
Replaced ground near alternator
Replaced cable from positive battery terminal to fusebox
Cleaned alternator plug
Replaced ~2ft of B terminal wire from alternator

Issue still remained.

Took the truck into an auto electrician while I was having the issue. He said I had a poor quality replacement alternator and I needed to get a OEM alternator. Did that and installed it yesterday.

Saw the issue again today...

Im pretty sure Ive mentioned this before, but I HATE electrical and after a year and a half of trying to fix this issue Im pretty sure it hates me just as much.