99 F250 Electrical Issues

So I have a 1999 Ford F250 Superduty with 2 batteries. It has the 7.3 of course. I'm having an electrical issue. I have 2 brand new batteries and a brand new alternator but I keep walking out to dead batteries. About a week ago I was driving and I heard a loud "pop" that sounded like it came from down under the dash but I couldn't find anything. After that I hadn't notice anything but then the truck started hesitating starting a little and then this morning it was dead. I have a new alternator and 2 new batteries so i'm confused. Nothing was left on, all lights were off. When I came back to the truck this afternoon there was a clicking coming from the fuse box underneath the dash. I know it had been previously replaced. So i'm basically stuck, I have no idea what it could be.
Any help would be greatly appreciated!
Gahhh seems like i'm fixing or repairing daily