2000 F350 Powerstoke Charging Problem

Alright, I have had enough. I have a 2000 Ford F-350 Powerstroke Diesel. About a month ago I noticed my batteries were dead after a few days. I removed battery terminals and cleaned them, as well as the power cables to and from the starter solenoid. Same thing again. I also started noticing that my voltmeter on the dash was very low in the normal range. So I removed both batteries and had them checked at my local O'Reilly store. Both batteries are three years old and both checked fine. I then removed my alternator and had it tested. It tested good in two tests. Since I was bored, I also removed my starter and had it tested. It also was good. Replaced them all, same thing. Since my alternator had a lifetime waranty, I replaced it. No change. I got my book out and found out I had no voltage coming to the alternator at the trigger wire. (light green with red stripe). I then traced the wire through the truck and found a broken wire at a connector behind the right side battery. It was some sort of plug that just had one wire loop. So, fixed that, had voltage to the trigger wire. Thought things were good. But now, I have a battery light coming on in the instrument panel. It slowly flashes at idle, and is on steady at higher rpm's. I checked the alternator with a voltmeter and found 14 volt output at all rpm's, but light is still on. Any suggestions? This is driving me crazy.