What are your batteries reading with the cables disconnected? On the glow plug relay you will have battery voltage on one large lug all the time. With the key on you should see battery voltage on one of the small lugs while the relay is energized and then on both of them once it turns off when the ground signal is removed.
Just for kicks I would take the truck to Auto Zone and have them do a battery load test and alternator test with everything still on the truck and see what they say.
96 F250 PS XLT 4X4 long box, 5sp,4.10, manual hubs,pyro+boost guages, Dark Toumaline, add a leaf, Dale's TYMAR, and HX hose, downpipe, coolant filter, Luk clutch