I did a complete wiring harness switch in my 85 f350 cc dually 6.9 with zf5 when i first started the truck after the switch one of the little yellow wires coming from the.voltage regulator the one that goes to the diode looking thing burned up, but it was still charging... I put over 200 miles on the truck and then suddenly no charge, and it was the wire that connects to the alternator... And it charged the batteries again and after it charged it won't charge the batteries anymore, and i have checked all the connections, the other yellow wire looks kinda toasty but its not completely burnt, just looking for ideas on where to start, and just 3 days ago alternator tested good on a bench tester at advance auto.parts

 

I just went through a similar issue. All of my connections were bad, including the ground from the frame of the regulator to the chasis and battery. My yellow wire to my regulator was discolored. My alternator would only charge 25 amperes out of 100amperes when the regulator was bypassed. So, I pulled my alternator apart only to find over 100 fully cooked gremlins (stink bugs) estimated, packed in around the brushes and the wiring. Everything is charging right now, even my charging gauge has started working now.
EDIT: The regulator frame requires a ground to the frame. There are a number of fusible links (square rubber) in the charging circuit. If these are bad, just cut out and replace with a fuse connector and the proper size fuse.