08 Pontiac wave Please help

Hi, i did something really dumb yesterday. I bought a new battery and put it on backwards(reverse polarity). The car started fine once i corrected it, but upon starting there were new lights illuminated. the battery light, the brake light and check engine light. Also there was only one gear available and shifter would not go out of park, also speedometer was dead.. i think it went into limp mode. i solved the speedometer and only 1 gear issue as there was a fuse in the dash that was dead. ECM/TCM fuse. Everything else seems ok. Except it's not charging. Probably the alternator but maybe a fuse. Can u tell me if there is an alternator fuse, i see nothing that says alt anywhere in the fuse boxes. There is a 100amp fuse next to the battery, i'm not sure if that's it or not. All the fuses look ok. Also there are black square thing in the box under the hood, could one of those have anything to do with the alternator?