I keep thinking about your mega fuse. You shorted the cable that goes directly to the battery. The mega fuse is there to protect everything upstream from that.... But the shirt would have to be over a hundred and some odd amps that the fuse is. Start simple. Replace the relays, double check all your fuses, take the alternator in to get it tested for free. I would almost bet money from past experience..... Lol, don't ask I was 19 years old..... But I would almost bet money the damage is in the alternator.
All the other electronic crap on today's vehicles is frightening. Stuff is sensitive.