Check and see if the altenator is getting 12V to both of the wires on the 2 prong plug with it running or the key in the "on" position..it needs 12V at both wires in order to energize the feld coil and make it charge,but if it lacks 12V at the white or tan wire on that plug ,it can still "self energize" when the altenator reaches about 2000 rpm,and it will suddenly "kick in" and start charging...the red wire in the two prong plug senses the voltage,and "tells" the regulator how much amps and volts to put out--if that wire is dead,it will likely go to "full charge" mode,and could be what your experiencing now..
You may want to check the glow plug wires before replacing the glow plugs,unless your certain it IS a bad glow plug...I've found many 6.2's have the glow plug wires get gangrene and corrode,and it reduces the voltage to the glow plug,if any at all gets thru them--the insulation will look like your blown fusible link and will feel "empty" where the wire failed...sometimes a test lamp might show voltage,but the wires are too corroded to let sufficient amperage pass to heat the glow plugs up--an old headlamp bulb is enough of a load to test if the wires are passing enough juice,if the lamp dont light or is dim,chances are that wire is corroded or burnt inside...
They sell 12V xircuit breakers ,I'd use them before a fuse on the main power wires--you definately dont want a fuse blowing while your on the highway,shutting everything down suddenly!...even a breaker could do the same though,so a fusible link wire is the proper way to fix it...I moved the twi thick red wires that go under the starter solenoid stud under the positive battery cable on my truck,and instead ran them to the positive battery terminal--I've had these wires burn up where they are routed thru the metal conduit near the exhaust,and the fusible links are inside that conduit,making it hard to inspect or repair them...GM used to run them to the battery terminal until 73,why they changed it to such a stupid design,I dont know...now all I have for wires at the starter solenoid is the positive battery cable,and the purple wire that activates the soleniod when you crank it over--a lot less chances of burnt wiring or failed fusible links that way...I left the fusible links intact and had to lengthen the wires in order to reach the battery positive terminal...