Looking at the wiring diagram, there are 3 fuses all next to each other at the battery.... an 80 amp and 2 60 amp fuses.... cable colours are red to the 80, red/blue trace to the 60 in the middle and red to the 60 next to that..

According to the diagram, the other side of the fuses to those wires (so basically they are connected to the buzbar that bolts to the battery terminal without going through any fuses) are the cables that go down to the alternator which ends up as 1 single cable...

Only the battery light goes through the fuse box.....have you connected a seperate volt meter to the battery? Don't go off the SECS for an accurate volt reading...