I would look at the alternator/regulator very close. Do the wires look burned up to either one? Just a guess, it could be possible that the welding internally shorted the diodes inside the alternator.
Do the FJ harnesses not have any fuesable links in the harness? Right next to the battery?
2004 4runner just starting to build
83 Hilux SR5 is being sold
94 pickup in a pile of parts